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 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2014.05.004
  • Structures With Same Primary Citation

  • 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, cat ...

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6
A
215Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petBalr3421
Find proteins for P0A384 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P0A384
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 4
B
160Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petDalr3422
Find proteins for Q93SX1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q93SX1
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome f
C
333Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petAall2452
Find proteins for Q93SW9 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q93SW9
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex iron-sulfur subunit 1
D
179Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petC1all2453
EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Find proteins for Q93SX0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q93SX0
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 6
E
31Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petLasl1922
Find proteins for Q8YVQ2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q8YVQ2
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 7
F
34Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petMasl4754
Find proteins for P0A3Y1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P0A3Y1
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 5
G
37Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petGasr1366
Find proteins for P58246 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58246
Protein Feature View
  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 8
H
29Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: petNasl4263
Find proteins for P61048 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P61048
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 17 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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B
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
OPC
Query on OPC

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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
 Ligand Interaction
SQD
Query on SQD

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

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

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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
 Ligand Interaction
3WM
Query on 3WM

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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
 Ligand Interaction
HEM
Query on HEM

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A, C
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
2WA
Query on 2WA

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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
 Ligand Interaction
7PH
Query on 7PH

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A, B, C, D, F
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
 Ligand Interaction
BCR
Query on BCR

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G
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
UMQ
Query on UMQ

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A, B, D, G
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
2WD
Query on 2WD

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

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A, B
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
 Ligand Interaction
MYS
Query on MYS

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D
PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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F
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • 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



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references