2ZT9 | pdb_00002zt9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120

PDB DOI: https://doi.org/10.2210/pdb2ZT9/pdb

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

Deposited: 2008-09-27 Released: 2009-02-10
Deposition Author(s): Craner, W.A., Baniulis, D., Yamashita, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.259 (Depositor), 0.256 (DCC)
R-Value Work:
0.230 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120

Baniulis, D., Yamashita, E., Whitelegge, J.P., Zatsman, A.I., Hendrich, M.P., Hasan, S.S., Ryan, C.M., Cramer, W.A.

(2009) J Biological Chem 284: 9861-9869

PubMed: 19189962 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M809196200
Primary Citation Related Structures:
2ZT9

PubMed Abstract:
The crystal structure of the cyanobacterial cytochrome b(6)f complex has previously been solved to 3.0-A resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b(6)f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b(6)f complex. Purified b(6)f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b(6)f complex, determined to a resolution of 3.0A (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b(p) that is rotated 180 degrees about the alpha- and gamma-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme c(n) is similar to that previously found in the b(6)f complex from other sources.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 114.2 kDa
Atom Count: 7,912
Modeled Residue Count: 959
Deposited Residue Count: 974
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	289	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: 1.10.99.1 (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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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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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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
OPC Query on OPC Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain U [auth H] MOL2 format, chain P [auth B] MOL2 format, chain U [auth H] mmCIF format, chain P [auth B] mmCIF format, chain U [auth H]	P [auth B], U [auth H]	(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 P [auth B] Focus chain U [auth H] Interactions & Density Focus chain P [auth B] Focus chain U [auth H]
SQD Query on SQD Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	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 Q [auth B] Interactions & Density Focus chain Q [auth B]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth C] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], R [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 R [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth C]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain T [auth G] MOL2 format, chain T [auth G] mmCIF format, chain T [auth G]	T [auth G]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain T [auth G] Interactions & Density Focus chain T [auth G]
UMQ Query on UMQ Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	L [auth A], M [auth A], N [auth A]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.259 (Depositor), 0.256 (DCC)
R-Value Work: 0.230 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.225	α = 90
b = 159.225	β = 90
c = 365.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-10

Deposition Author(s):

Craner, W.A.

Baniulis, D.

Yamashita, E.

Revision History (Full details and data files)

Version 1.0: 2009-02-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2013-12-11
Changes: Database references
Version 1.3: 2018-06-20
Changes: Data collection, Structure summary
Version 1.4: 2019-10-02
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
Version 2.1: 2024-11-20
Changes: Structure summary

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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.

2ZT9 | pdb_00002zt9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120

Literature

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120

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)