8BPX

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution.

Klusch, N.Dreimann, M.Senkler, J.Rugen, N.Kuhlbrandt, W.Braun, H.P.

(2023) Nat Plants 9: 142-156

  • DOI: https://doi.org/10.1038/s41477-022-01308-6
  • Primary Citation of Related Structures:  
    8BED, 8BEE, 8BEF, 8BEH, 8BEL, 8BEP, 8BPX, 8BQ5, 8BQ6

  • PubMed Abstract: 

    Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III 2 with a co-purified ubiquinone in the Q O site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.


  • Organizational Affiliation

    Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany. Niklas.Klusch@biophys.mpg.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3119Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P92533 (Arabidopsis thaliana)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial218Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q42577 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3190Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2394Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for P93306 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial255Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial486Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9FNN5 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial748Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1325Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial222Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6205Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P60497 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L100Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for Q04614 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5669Arabidopsis thalianaMutation(s): 3 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P29388 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4495Arabidopsis thalianaMutation(s): 3 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2499Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O05000 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
2Fe-2S ferredoxin-like superfamily protein159Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SRR8 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial402Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SK66 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial154Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9FJW4 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial110Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9M9M6 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 297Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FIJ2 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 1, mitochondrial122Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53665 (Arabidopsis thaliana)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 2, mitochondrial126Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O80800 (Arabidopsis thaliana)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial169Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FLX7 (Arabidopsis thaliana)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6133Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9LHI0 (Arabidopsis thaliana)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B106Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Outer envelope pore protein 16-3, chloroplastic/mitochondrial159Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O48528 (Arabidopsis thaliana)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q8RWA7 (Arabidopsis thaliana)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]65Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C9Z5 (Arabidopsis thaliana)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
At2g46540/F11C10.23BA [auth b]65Arabidopsis thalianaMutation(s): 0 
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Find proteins for Q9ZPY5 (Arabidopsis thaliana)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinCA [auth c]88Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Excitatory amino acid transporterDA [auth d]81Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q94AL6 (Arabidopsis thaliana)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-BEA [auth e]83Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9LZI6 (Arabidopsis thaliana)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
At4g16450FA [auth f]106Arabidopsis thalianaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) proteinGA [auth g]114Arabidopsis thalianaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
At1g67350HA [auth i]98Arabidopsis thalianaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2IA [auth j]69Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-AJA [auth k]72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O64725 (Arabidopsis thaliana)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialKA [auth l]125Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FGK0 (Arabidopsis thaliana)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
AT2G31490 proteinLA [auth m]71Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9SIQ8 (Arabidopsis thaliana)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth n]117Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q945M1 (Arabidopsis thaliana)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7NA [auth o]103Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9SKC9 (Arabidopsis thaliana)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-BOA [auth p]106Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12PA [auth q]159Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At1g67785QA [auth u]63Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At2g27730, mitochondrialRA [auth v]113Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9ZUX4 (Arabidopsis thaliana)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZUX4
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase-like 2, mitochondrialSA [auth x]256Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SMN1 (Arabidopsis thaliana)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 2, mitochondrialTA [auth y]278Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9C6B3 (Arabidopsis thaliana)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 1, mitochondrialUA [auth z]275Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9FWR5 (Arabidopsis thaliana)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrialFB [auth BA],
VA [auth AA]
503Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9ZU25 (Arabidopsis thaliana)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit beta, mitochondrialGB [auth BB],
WA [auth AB]
531Arabidopsis thalianaMutation(s): 0 
EC: 3.4.24.64
Membrane Entity: Yes 
UniProt
Find proteins for Q42290 (Arabidopsis thaliana)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bHB [auth BC],
XA [auth AC]
393Arabidopsis thalianaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P42792 (Arabidopsis thaliana)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske-1, mitochondrialIB [auth BD],
YA [auth AD]
272Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q94JS0 (Arabidopsis thaliana)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1 2, heme protein, mitochondrialJB [auth BE],
ZA [auth AE]
307Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FKS5 (Arabidopsis thaliana)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7-2, mitochondrialAB [auth AF],
KB [auth BF]
122Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F4JWS8 (Arabidopsis thaliana)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8-1, mitochondrialBB [auth AG],
LB [auth BG]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SG91 (Arabidopsis thaliana)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6-1, mitochondrialCB [auth AH],
MB [auth BH]
69Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q0WWE3 (Arabidopsis thaliana)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialDB [auth AI],
NB [auth BI]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LXJ2 (Arabidopsis thaliana)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialEB [auth AJ],
OB [auth BJ]
57Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q94K78 (Arabidopsis thaliana)
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
DE [auth AE]
HD [auth u]
ID [auth u]
PE [auth BC]
QE [auth BC]
DE [auth AE],
HD [auth u],
ID [auth u],
PE [auth BC],
QE [auth BC],
XE [auth BE],
YD [auth AC],
ZD [auth AC],
ZE [auth BG]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Q7G (Subject of Investigation/LOI)
Query on Q7G

Download Ideal Coordinates CCD File 
CC [auth K]
OC [auth M]
SE [auth BC]
TE [auth BC]
ZB [auth H]
CC [auth K],
OC [auth M],
SE [auth BC],
TE [auth BC],
ZB [auth H],
ZC [auth a]
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
C56 H92 O25
LKBFXDNKNZXHHW-NXLTVWPKSA-N
COO (Subject of Investigation/LOI)
Query on COO

Download Ideal Coordinates CCD File 
LD [auth y]CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
UQ9 (Subject of Investigation/LOI)
Query on UQ9

Download Ideal Coordinates CCD File 
YB [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC7 (Subject of Investigation/LOI)
Query on PC7

Download Ideal Coordinates CCD File 
AE [auth AC]
BD [auth d]
ED [auth f]
FE [auth AG]
IC [auth L]
AE [auth AC],
BD [auth d],
ED [auth f],
FE [auth AG],
IC [auth L],
JD [auth v],
QD [auth AB],
RE [auth BC],
VE [auth BD]
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-FAIXQHPJSA-O
PGT (Subject of Investigation/LOI)
Query on PGT

Download Ideal Coordinates CCD File 
EC [auth L]
EE [auth AF]
FC [auth L]
GC [auth L]
LC [auth M]
EC [auth L],
EE [auth AF],
FC [auth L],
GC [auth L],
LC [auth M],
MD [auth y],
OE [auth BC],
PB [auth A],
WD [auth AC],
XD [auth AC]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
TC [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
AD [auth d]
GD [auth m]
HC [auth L]
IE [auth BB]
MC [auth M]
AD [auth d],
GD [auth m],
HC [auth L],
IE [auth BB],
MC [auth M],
NC [auth M],
ND [auth z],
PC [auth N],
PD [auth AB],
QC [auth N],
RB [auth D],
RC [auth N],
YC [auth Y],
YE [auth BF]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH

Download Ideal Coordinates CCD File 
AF [auth BJ]
BF [auth BJ]
CD [auth f]
DC [auth L]
DD [auth f]
AF [auth BJ],
BF [auth BJ],
CD [auth f],
DC [auth L],
DD [auth f],
FD [auth l],
GE [auth AI],
KC [auth M],
NE [auth BC],
VD [auth AC],
XC [auth Y]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
UQ7 (Subject of Investigation/LOI)
Query on UQ7

Download Ideal Coordinates CCD File 
ME [auth BC]UBIQUINONE-7
C44 H66 O4
DBESHHFMIFSNRV-RJYQSXAYSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
CE [auth AE]
JE [auth BC]
KE [auth BC]
RD [auth AC]
SD [auth AC]
CE [auth AE],
JE [auth BC],
KE [auth BC],
RD [auth AC],
SD [auth AC],
WE [auth BE]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
VC [auth T],
WC [auth W]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
UQ5 (Subject of Investigation/LOI)
Query on UQ5

Download Ideal Coordinates CCD File 
JC [auth L],
LE [auth BC],
TD [auth AC],
UD [auth AC]
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
C34 H50 O4
NYFAQDMDAFCWPU-UVCHAVPFSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
TB [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AC [auth I]
BC [auth I]
QB [auth B]
UB [auth F]
WB [auth G]
AC [auth I],
BC [auth I],
QB [auth B],
UB [auth F],
WB [auth G],
XB [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
BE [auth AD],
SB [auth E],
UE [auth BD],
VB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
HE [auth BB],
KD [auth y],
OD [auth AB],
UC [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
SC [auth O]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONRELION3.1.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary
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