1Q90

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii

PDB DOI: https://doi.org/10.2210/pdb1Q90/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Chlamydomonas reinhardtii
Expression System: Chlamydomonas reinhardtii
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2003-08-22 Released: 2003-12-09
Deposition Author(s): Stroebel, D., Choquet, Y., Popot, J.-L., Picot, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.261
R-Value Work: 0.222
R-Value Observed: 0.222

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

An Atypical Haem in the Cytochrome B6F Complex

Stroebel, D., Choquet, Y., Popot, J.-L., Picot, D.

(2003) Nature 426: 413-418

PubMed: 14647374 Search on PubMed
DOI: https://doi.org/10.1038/nature02155
Primary Citation of Related Structures:
1Q90

PubMed Abstract:
Photosystems I and II (PSI and II) are reaction centres that capture light energy in order to drive oxygenic photosynthesis; however, they can only do so by interacting with the multisubunit cytochrome b(6)f complex. This complex receives electrons from PSII and passes them to PSI, pumping protons across the membrane and powering the Q-cycle. Unlike the mitochondrial and bacterial homologue cytochrome bc(1), cytochrome b(6)f can switch to a cyclic mode of electron transfer around PSI using an unknown pathway. Here we present the X-ray structure at 3.1 A of cytochrome b(6)f from the alga Chlamydomonas reinhardtii. The structure bears similarities to cytochrome bc(1) but also exhibits some unique features, such as binding chlorophyll, beta-carotene and an unexpected haem sharing a quinone site. This haem is atypical as it is covalently bound by one thioether linkage and has no axial amino acid ligand. This haem may be the missing link in oxygenic photosynthesis.

Organizational Affiliation

Laboratoire de Physico-Chimie Moléculaire des Membranes Biologiques, CNRS/Université Paris 7, UMR 7099, France.

Macromolecule Content

Total Structure Weight: 113.86 kDa
Atom Count: 7,778
Modelled Residue Count: 952
Deposited Residue Count: 981
Unique protein chains: 9

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apocytochrome f	A	292	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETA Membrane Entity: Yes
UniProt
Find proteins for P23577 (Chlamydomonas reinhardtii) Explore P23577 Go to UniProtKB: P23577
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23577
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6	B	215	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETB Membrane Entity: Yes
UniProt
Find proteins for Q00471 (Chlamydomonas reinhardtii) Explore Q00471 Go to UniProtKB: Q00471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00471
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome B6-F complex iron-sulfur subunit	C	127	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETC EC: 1.10.99.1 Membrane Entity: Yes
UniProt
Find proteins for P49728 (Chlamydomonas reinhardtii) Explore P49728 Go to UniProtKB: P49728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49728
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 4	D	159	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETD Membrane Entity: Yes
UniProt
Find proteins for P23230 (Chlamydomonas reinhardtii) Explore P23230 Go to UniProtKB: P23230
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23230
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome B6-F complex iron-sulfur subunit	E [auth R]	49	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETC EC: 1.10.99.1 Membrane Entity: Yes
UniProt
Find proteins for P49728 (Chlamydomonas reinhardtii) Explore P49728 Go to UniProtKB: P49728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49728
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6f complex subunit petG	F [auth G]	37	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETG Membrane Entity: Yes
UniProt
Find proteins for Q08362 (Chlamydomonas reinhardtii) Explore Q08362 Go to UniProtKB: Q08362
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08362
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6f complex subunit petL	G [auth L]	32	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETL Membrane Entity: Yes
UniProt
Find proteins for P50369 (Chlamydomonas reinhardtii) Explore P50369 Go to UniProtKB: P50369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50369
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6f complex subunit PETM	H [auth M]	39	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETM Membrane Entity: Yes
UniProt
Find proteins for Q42496 (Chlamydomonas reinhardtii) Explore Q42496 Go to UniProtKB: Q42496
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q42496
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6f complex subunit PETN	I [auth N]	31	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: PETN Membrane Entity: Yes
UniProt
Find proteins for P0C1D4 (Chlamydomonas reinhardtii) Explore P0C1D4 Go to UniProtKB: P0C1D4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C1D4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D]	Q [auth D]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
SQD Query on SQD Download Ideal Coordinates CCD File SDF format, chain T [auth R] MOL2 format, chain T [auth R]	T [auth R]	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 T [auth R] Interactions & Density Focus chain T [auth R]
LMG Query on LMG Download Ideal Coordinates CCD File SDF format, chain U [auth L] SDF format, chain S [auth D] MOL2 format, chain U [auth L] MOL2 format, chain S [auth D]	S [auth D], U [auth L]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain S [auth D] Focus chain U [auth L] Interactions & Density Focus chain S [auth D] Focus chain U [auth L]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	J [auth A], K [auth B], L [auth B], M [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
BCR Query on BCR Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
TDS Query on TDS Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D]	R [auth D]	8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE C₂₅ H₃₈ O₅ LSHATXKKRQGSEC-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B]	O [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C]	P [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.261
R-Value Work: 0.222
R-Value Observed: 0.222
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.454	α = 90
b = 171.205	β = 90
c = 351.009	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
MLPHARE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-12-09
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2012-07-25
Changes: Non-polymer description
Version 2.0: 2021-03-03
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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1Q90

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii

An Atypical Haem in the Cytochrome B6F Complex

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

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)