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 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


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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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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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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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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
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UniProt GroupD2Z0P9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 alpha polypeptide61Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupD2Z0P2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
High-potential iron-sulfur proteinKA [auth b]83Thermochromatium tepidumMutation(s): 0 
UniProt
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UniProt GroupP80176
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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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 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.435α = 90
b = 183.335β = 112.584
c = 123.857γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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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