7C52

Co-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 ?
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP.

Kawakami, T.Yu, L.J.Liang, T.Okazaki, K.Madigan, M.T.Kimura, Y.Wang-Otomo, Z.Y.

(2021) Nat Commun 12: 1104-1104

  • DOI: https://doi.org/10.1038/s41467-021-21397-9
  • Primary Citation of Related Structures:  
    7C52

  • PubMed Abstract: 

    Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems.


  • Organizational Affiliation

    Faculty of Science, Ibaraki University, Mito, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]311Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P5 (Thermochromatium tepidum)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitB [auth L]281Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P3 (Thermochromatium tepidum)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitC [auth M]325Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8ASG6 (Thermochromatium tepidum)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8ASG6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]259Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P9 (Thermochromatium tepidum)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 alpha polypeptide61Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum)
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Entity Groups  
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UniProt GroupD2Z0P1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
High-potential iron-sulfur proteinKA [auth b]83Thermochromatium tepidumMutation(s): 0 
UniProt
Find proteins for P80176 (Thermochromatium tepidum)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80176
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  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
DE [auth 1]
FC [auth D]
GC [auth D]
ID [auth S]
JB [auth M]
DE [auth 1],
FC [auth D],
GC [auth D],
ID [auth S],
JB [auth M],
ND [auth U],
PB [auth M],
WB [auth H],
YD [auth Y],
ZC [auth O]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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AE [auth 1]
BD [auth P]
CC [auth D]
CD [auth Q]
EB [auth M]
AE [auth 1],
BD [auth P],
CC [auth D],
CD [auth Q],
EB [auth M],
EC [auth D],
ED [auth Q],
FD [auth S],
GE [auth 2],
HD [auth S],
HE [auth 3],
IC [auth F],
KC [auth F],
KD [auth U],
MC [auth I],
MD [auth U],
NE [auth 4],
OE [auth 5],
PD [auth W],
QC [auth J],
QE [auth 5],
RC [auth K],
RE [auth 7],
SD [auth W],
TA [auth L],
TC [auth K],
TE [auth 7],
UA [auth L],
VD [auth Y],
VE [auth 9],
WC [auth O],
XA [auth L],
XB [auth A],
XD [auth Y],
XE [auth 9],
ZB [auth A]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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FB [auth M],
VA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV
Query on PGV

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AB [auth L]
EE [auth 1]
HC [auth D]
LE [auth 3]
NB [auth M]
AB [auth L],
EE [auth 1],
HC [auth D],
LE [auth 3],
NB [auth M],
OB [auth M],
SA [auth C],
UB [auth H],
YE [auth 9],
ZA [auth L]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
UQ8
Query on UQ8

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BB [auth L],
CB [auth L],
DB [auth L],
QB [auth M],
WA [auth L]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
LHG
Query on LHG

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RA [auth C]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MQ8
Query on MQ8

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HB [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF
Query on PEF

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CE [auth 1]
KB [auth M]
KE [auth 3]
LB [auth M]
MB [auth M]
CE [auth 1],
KB [auth M],
KE [auth 3],
LB [auth M],
MB [auth M],
OC [auth I],
TB [auth H],
TD [auth W],
UC [auth K],
UD [auth W]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CRT
Query on CRT

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AC [auth A]
AD [auth P]
BC [auth B]
FE [auth 2]
IB [auth M]
AC [auth A],
AD [auth P],
BC [auth B],
FE [auth 2],
IB [auth M],
JD [auth T],
JE [auth 3],
LC [auth G],
ME [auth 4],
OD [auth V],
PC [auth J],
QD [auth W],
UE [auth 8],
VC [auth N],
YC [auth O],
ZD [auth Z],
ZE [auth 0]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT

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RB [auth M],
VB [auth H]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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AF [auth b]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4
Query on SO4

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YA [auth L]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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QA [auth C],
SB [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

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GB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

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BE [auth 1]
DC [auth D]
DD [auth Q]
GD [auth S]
IE [auth 3]
BE [auth 1],
DC [auth D],
DD [auth Q],
GD [auth S],
IE [auth 3],
JC [auth F],
LD [auth U],
NC [auth I],
PA [auth C],
PE [auth 5],
RD [auth W],
SC [auth K],
SE [auth 7],
WD [auth Y],
WE [auth 9],
XC [auth O],
YB [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 ?
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 96.435¦Á = 90
b = 183.335¦Â = 112.584
c = 123.857¦Ã = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
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