4OGQ

Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CLAClick on this verticalbar to view detailsBest fitted OPCClick on this verticalbar to view detailsBest fitted SQDClick on this verticalbar to view detailsBest fitted 1O2Click on this verticalbar to view detailsBest fitted 2WMClick on this verticalbar to view detailsBest fitted 3WMClick on this verticalbar to view detailsBest fitted HECClick on this verticalbar to view detailsBest fitted 2WAClick on this verticalbar to view detailsBest fitted 7PHClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted UMQClick on this verticalbar to view detailsBest fitted 2WDClick on this verticalbar to view detailsBest fitted 8K6Click on this verticalbar to view detailsBest fitted MYSClick on this verticalbar to view details

This is version 3.0 of the entry. See complete history


Literature

Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex.

Hasan, S.S.Cramer, W.A.

(2014) Structure 22: 1008-1015

  • DOI: https://doi.org/10.1016/j.str.2014.05.004
  • Primary Citation of Related Structures:  
    4OGQ

  • PubMed Abstract: 

    The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein complexes is poorly understood. The dimeric photosynthetic cytochrome b6f complex, a 16-mer of eight distinct subunits and 26 transmembrane helices, catalyzes transmembrane proton-coupled electron transfer for energy storage. Using a 2.5 Å crystal structure of the dimeric complex, we identified 23 distinct lipid-binding sites per monomer. Annular lipids are proposed to provide a connection for super-complex formation with the photosystem-I reaction center and the LHCII kinase enzyme for transmembrane signaling. Internal lipids mediate crosslinking to stabilize the domain-swapped iron-sulfur protein subunit, dielectric heterogeneity within intermonomer and intramonomer electron transfer pathways, and dimer stabilization through lipid-mediated intermonomer interactions. This study provides a complete structure analysis of lipid-mediated functions in a multi-subunit membrane protein complex and reveals lipid sites at positions essential for assembly and function.


  • Organizational Affiliation

    Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, IN 47907, USA. Electronic address: syedsaifhasan@gmail.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A384 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP0A384
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4160Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93SX1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupQ93SX1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f333Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93SW9 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit 1179Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q93SX0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupQ93SX0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 631Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YVQ2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 734Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A3Y1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 537Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58246 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 829Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61048 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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U [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OPC
Query on OPC

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V [auth B](7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
SQD
Query on SQD

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DA [auth D]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
1O2
Query on 1O2

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JA [auth F](2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate
C43 H80 O10
JBZBYHKCRFIXBI-BNOJPGAFSA-N
2WM
Query on 2WM

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Q [auth A](1S,8E)-1-{[(2S)-3-hydroxy-2-{[(1S)-1-hydroxyoctadecyl]oxy}propyl]oxy}octadec-8-en-1-ol
C39 H78 O5
IYPOYOCNVQYKRB-UUYGCZLBSA-N
3WM
Query on 3WM

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GA [auth E](1S,8E,1'R,8'Z)-1,1'-{[(2S)-3-hydroxypropane-1,2-diyl]bis(oxy)}bisoctadec-8-en-1-ol
C39 H76 O5
OBURSNHVDFVKSA-YKKXEANNSA-N
HEC
Query on HEC

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I [auth A],
J [auth A],
K [auth A],
X [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
2WA
Query on 2WA

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HA [auth F](1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol
C35 H70 O5
YLBOKUFLARRKAJ-FAMWHJLKSA-N
7PH
Query on 7PH

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CA [auth D],
KA [auth F],
M [auth A],
W [auth B],
Z [auth C]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
BCR
Query on BCR

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MA [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

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AA [auth D],
L [auth A],
LA [auth G],
R [auth B],
T [auth B]
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
2WD
Query on 2WD

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FA [auth D](1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol
C14 H30 O5
GKBWBGWQSQJUDA-BFHYXJOUSA-N
8K6
Query on 8K6

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N [auth A],
O [auth A],
P [auth A],
S [auth B]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
MYS
Query on MYS

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BA [auth D]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
FES
Query on FES

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EA [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
OCT
Query on OCT

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IA [auth F]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CD
Query on CD

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Y [auth C]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.228α = 90
b = 159.228β = 90
c = 365.879γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CLAClick on this verticalbar to view detailsBest fitted OPCClick on this verticalbar to view detailsBest fitted SQDClick on this verticalbar to view detailsBest fitted 1O2Click on this verticalbar to view detailsBest fitted 2WMClick on this verticalbar to view detailsBest fitted 3WMClick on this verticalbar to view detailsBest fitted HECClick on this verticalbar to view detailsBest fitted 2WAClick on this verticalbar to view detailsBest fitted 7PHClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted UMQClick on this verticalbar to view detailsBest fitted 2WDClick on this verticalbar to view detailsBest fitted 8K6Click on this verticalbar to view detailsBest fitted MYSClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary