9F5Y | pdb_00009f5y

Structure of the Chlamydomonas reinhardtii respiratory complex I from respiratory supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In-cell architecture of the mitochondrial respiratory chain.

Waltz, F.Righetto, R.D.Lamm, L.Salinas-Giege, T.Kelley, R.Zhang, X.Obr, M.Khavnekar, S.Kotecha, A.Engel, B.D.

(2025) Science 387: 1296-1301

  • DOI: https://doi.org/10.1126/science.ads8738
  • Primary Citation of Related Structures:  
    9F5X, 9F5Y, 9F5Z, 9F60, 9F61, 9F62

  • PubMed Abstract: 

    Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in Chlamydomonas reinhardtii cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (?) resolution structure showing binding of electron carrier cytochrome c . Combined with single-particle cryo-electron microscopy at 2.4-? resolution, we model how the respiratory complexes organize inside native mitochondria.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 24 kD subunit282Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial484Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 78 kDa subunit733Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein282Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 49 kD subunit467Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit 10164Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit 8231Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
B14.5a118Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit165Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinJ,
RA [auth r]
128Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase B14 subunit138Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial187Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 13 kD-like subunit154Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12156Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase B8 subunit101Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 39 kDa subunit397Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1292Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2387Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3279Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4443Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 4L227Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5546Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6162Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ASHI149Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
P964Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
KFYI124Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
AGGGAA [auth a]129Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ESSSBA [auth b]172Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
B9CA [auth c]67Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunitDA [auth d]86Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunitEA [auth e]219Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunitFA [auth f]65Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunitGA [auth g]55Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunitHA [auth h]142Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 15 kDa subunit-likeIA [auth i]81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7JA [auth j]86Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9KA [auth k]117Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 20,9 kD-like subunitLA [auth l]121Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13MA [auth m]142Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunitNA [auth n]106Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q6V504 (Chlamydomonas reinhardtii)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunitOA [auth o]155Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q6V505 (Chlamydomonas reinhardtii)
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UniProt GroupQ6V505
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunitPA [auth p]130Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6QAY0 (Chlamydomonas reinhardtii)
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UniProt GroupQ6QAY0
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunitQA [auth q]197Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6QAY1 (Chlamydomonas reinhardtii)
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UniProt GroupQ6QAY1
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunitSA [auth s]312Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6S7R7 (Chlamydomonas reinhardtii)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
CAG2 - CA-likeTA [auth t]279Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JFK6 (Chlamydomonas reinhardtii)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
CAG1UA [auth u]229Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JHY4 (Chlamydomonas reinhardtii)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
P10VA [auth v]45Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunitWA [auth w]109Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6QAY5 (Chlamydomonas reinhardtii)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP8XA [auth x]157Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IS53 (Chlamydomonas reinhardtii)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP7YA [auth y]118Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JA22 (Chlamydomonas reinhardtii)
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
AD [auth y]
DC [auth V]
HC [auth W]
PC [auth h]
RB [auth R]
AD [auth y],
DC [auth V],
HC [auth W],
PC [auth h],
RB [auth R],
VC [auth u],
WC [auth u],
YC [auth x]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
COO
Query on COO

Download Ideal Coordinates CCD File 
SC [auth s]CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
PC7
Query on PC7

Download Ideal Coordinates CCD File 
MB [auth Q],
PB [auth R],
UC [auth u],
XB [auth T]
(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
Query on PGT

Download Ideal Coordinates CCD File 
IC [auth b],
QC [auth l],
WB [auth T],
ZB [auth T]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
KB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
AC [auth T]
EC [auth V]
FC [auth V]
GC [auth V]
IB [auth G]
AC [auth T],
EC [auth V],
FC [auth V],
GC [auth V],
IB [auth G],
KC [auth e],
LC [auth e],
OB [auth R],
OC [auth h],
QB [auth R],
SB [auth R],
UB [auth S],
VB [auth T],
YB [auth T],
ZC [auth x]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
BC [auth V]
CC [auth V]
JC [auth c]
MC [auth g]
NB [auth R]
BC [auth V],
CC [auth V],
JC [auth c],
MC [auth g],
NB [auth R],
NC [auth h],
TB [auth S],
XC [auth w]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
8Q1
Query on 8Q1

Download Ideal Coordinates CCD File 
JB [auth J],
RC [auth r]
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
Query on UQ5

Download Ideal Coordinates CCD File 
LB [auth Q]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
Query on FMN

Download Ideal Coordinates CCD File 
AB [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BB [auth B]
DB [auth C]
EB [auth C]
FB [auth F]
GB [auth G]
BB [auth B],
DB [auth C],
EB [auth C],
FB [auth F],
GB [auth G],
HB [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
CB [auth C],
ZA [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
TC [auth s]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermany--
Swiss National Science FoundationSwitzerland210561

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
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