4I7Z | pdb_00004i7z

Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain

PDB DOI: https://doi.org/10.2210/pdb4I7Z/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Mastigocladus laminosus
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2012-12-01 Released: 2013-04-17
Deposition Author(s): Hasan, S.S., Stofleth, J.T., Yamashita, E., Cramer, W.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.272 (Depositor), 0.278 (DCC)
R-Value Work:
0.248 (Depositor), 0.255 (DCC)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.

Hasan, S.S., Stofleth, J.T., Yamashita, E., Cramer, W.A.

(2013) Biochemistry 52: 2649-2654

PubMed: 23514009 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi301638h
Primary Citation Related Structures:
4I7Z

PubMed Abstract:
Cytochrome b6f catalyzes quinone redox reactions within photosynthetic membranes to generate a transmembrane proton electrochemical gradient for ATP synthesis. A key step involves the transfer of an electron from the [2Fe-2S] cluster of the iron-sulfur protein (ISP) extrinsic domain to the cytochrome f heme across a distance of 26 Å, which is too large for competent electron transfer but could be bridged by translation-rotation of the ISP. Here we report the first crystallographic evidence of significant motion of the ISP extrinsic domain. It is inferred that extensive crystallographic disorder of the ISP extrinsic domain indicates conformational flexibility. The ISP disorder observed in this structure, in contrast to the largely ordered ISP structure observed in the b6f complex supplemented with neutral lipids, is attributed to electrostatic interactions arising from anionic lipids.

Organizational Affiliation

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecule Content

Total Structure Weight: 116.43 kDa
Atom Count: 6,959
Modeled Residue Count: 820
Deposited Residue Count: 976
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	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83791 (Mastigocladus laminosus) Explore P83791 Go to UniProtKB: P83791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83791
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	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83792 (Mastigocladus laminosus) Explore P83792 Go to UniProtKB: P83792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83792
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Apocytochrome f	C	289	Mastigocladus laminosus	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for P83793 (Mastigocladus laminosus) Explore P83793 Go to UniProtKB: P83793
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83793
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	D	179	Mastigocladus laminosus	Mutation(s): 0 EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P83794 (Mastigocladus laminosus) Explore P83794 Go to UniProtKB: P83794
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83794
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	32	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83795 (Mastigocladus laminosus) Explore P83795 Go to UniProtKB: P83795
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83795
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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	35	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83796 (Mastigocladus laminosus) Explore P83796 Go to UniProtKB: P83796
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83796
Sequence Annotations Expand
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	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83797 (Mastigocladus laminosus) Explore P83797 Go to UniProtKB: P83797
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83797
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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	Mastigocladus laminosus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P83798 (Mastigocladus laminosus) Explore P83798 Go to UniProtKB: P83798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83798
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
OZ2 Query on OZ2 Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain T [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C]	AA [auth G], T [auth B], W [auth C]	(2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate C₃₇ H₆₉ O₁₀ P YOPHQENQMRACBJ-BMAOJOIDSA-N		Interactions Focus chain AA [auth G] Focus chain T [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth G] Focus chain T [auth B] Focus chain W [auth C]
HEM Query on HEM 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 U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain U [auth C]	I [auth A], J [auth A], K [auth A], U [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth C]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain Z [auth G]	Z [auth G]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain Z [auth G] Interactions & Density Focus chain Z [auth G]
UMQ Query on UMQ Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	N [auth A], O [auth A], P [auth A]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
1E2 Query on 1E2 Download:Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	(2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside C₁₁ H₂₀ O₁₁ S GWOURQAWIHLHOD-MPVQUNCYSA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
8K6 Query on 8K6 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MYS Query on MYS Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Y [auth F]	Y [auth F]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C]	Q [auth A], S [auth B], V [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain S [auth B] Focus chain V [auth C] Interactions & Density Focus chain Q [auth A] Focus chain S [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.272 (Depositor), 0.278 (DCC)
R-Value Work: 0.248 (Depositor), 0.255 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.451	α = 90
b = 159.451	β = 90
c = 362.746	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing
JBluIce-EPICS	data collection

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2013-12-04
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Refinement description
Version 2.0: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Non-polymer description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4I7Z | pdb_00004i7z

Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain

Literature

Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.

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)