4OGQ | pdb_00004ogq

Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex

PDB DOI: https://doi.org/10.2210/pdb4OGQ/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2014-01-16 Released: 2014-05-14
Deposition Author(s): Hasan, S.S., Cramer, W.A.

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

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

PubMed: 24931468 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2014.05.004
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 126.32 kDa
Atom Count: 8,396
Modeled Residue Count: 949
Deposited Residue Count: 1,018
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6	A	215	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A384 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P0A384 Go to UniProtKB: P0A384
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A384
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 4	B	160	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q93SX1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q93SX1 Go to UniProtKB: Q93SX1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93SX1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Apocytochrome f	C	333	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q93SW9 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q93SW9 Go to UniProtKB: Q93SW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93SW9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex iron-sulfur subunit 1	D	179	Nostoc sp. PCC 7120 = FACHB-418	Mutation(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)) Explore Q93SX0 Go to UniProtKB: Q93SX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93SX0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 6	E	31	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8YVQ2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YVQ2 Go to UniProtKB: Q8YVQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YVQ2
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 7	F	34	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A3Y1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P0A3Y1 Go to UniProtKB: P0A3Y1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A3Y1
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 5	G	37	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P58246 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P58246 Go to UniProtKB: P58246
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58246
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 8	H	29	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P61048 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P61048 Go to UniProtKB: P61048
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61048
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 17 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
OPC Query on OPC Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	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		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
SQD Query on SQD Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain DA [auth D]	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		Interactions Focus chain DA [auth D] Interactions & Density Focus chain DA [auth D]
1O2 Query on 1O2 Download:Ideal Coordinates CCD File SDF format, chain JA [auth F] MOL2 format, chain JA [auth F] mmCIF format, chain JA [auth F]	JA [auth F]	(2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate C₄₃ H₈₀ O₁₀ JBZBYHKCRFIXBI-BNOJPGAFSA-N		Interactions Focus chain JA [auth F] Interactions & Density Focus chain JA [auth F]
2WM Query on 2WM Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	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		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
3WM Query on 3WM Download:Ideal Coordinates CCD File SDF format, chain GA [auth E] MOL2 format, chain GA [auth E] mmCIF format, chain GA [auth E]	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		Interactions Focus chain GA [auth E] Interactions & Density Focus chain GA [auth E]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain X [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain X [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain X [auth C]	I [auth A], J [auth A], K [auth A], X [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth C]
2WA Query on 2WA Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	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		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]
7PH Query on 7PH Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain KA [auth F] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain KA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth C]	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		Interactions Focus chain CA [auth D] Focus chain KA [auth F] Focus chain M [auth A] Focus chain W [auth B] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain KA [auth F] Focus chain M [auth A] Focus chain W [auth B] Focus chain Z [auth C]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain MA [auth G] MOL2 format, chain MA [auth G] mmCIF format, chain MA [auth G]	MA [auth G]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain MA [auth G] Interactions & Density Focus chain MA [auth G]
UMQ Query on UMQ Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain R [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B]	AA [auth D], L [auth A], LA [auth G], R [auth B], T [auth B]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain AA [auth D] Focus chain L [auth A] Focus chain LA [auth G] Focus chain R [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth D] Focus chain L [auth A] Focus chain LA [auth G] Focus chain R [auth B] Focus chain T [auth B]
2WD Query on 2WD Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain FA [auth D]	FA [auth D]	(1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol C₁₄ H₃₀ O₅ GKBWBGWQSQJUDA-BFHYXJOUSA-N		Interactions Focus chain FA [auth D] Interactions & Density Focus chain FA [auth D]
8K6 Query on 8K6 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B]	N [auth A], O [auth A], P [auth A], S [auth B]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B]
MYS Query on MYS Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain BA [auth D]	BA [auth D]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Interactions & Density Focus chain BA [auth D]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain EA [auth D]	EA [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Interactions & Density Focus chain EA [auth D]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] MOL2 format, chain IA [auth F] mmCIF format, chain IA [auth F]	IA [auth F]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Interactions & Density Focus chain IA [auth F]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]

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 = 159.228	α = 90
b = 159.228	β = 90
c = 365.879	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Hasan, S.S.

Cramer, W.A.

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

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4OGQ | pdb_00004ogq

Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)