4H44

2.70 A Cytochrome b6f Complex Structure From Nostoc PCC 7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex

Hasan, S.S.Yamashita, E.Baniulis, D.Cramer, W.A.

(2013) Proc Natl Acad Sci U S A 110: 4297-4302

  • DOI: https://doi.org/10.1073/pnas.1222248110
  • Primary Citation of Related Structures:  
    4H0L, 4H13, 4H44

  • PubMed Abstract: 

    As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygenic photosynthesis is generated by the cytochrome b6f complex. The proton uptake pathway from the electrochemically negative (n) aqueous phase to the n-side quinone binding site of the complex, and a probable route for proton exit to the positive phase resulting from quinol oxidation, are defined in a 2.70-Å crystal structure and in structures with quinone analog inhibitors at 3.07 Å (tridecyl-stigmatellin) and 3.25-Å (2-nonyl-4-hydroxyquinoline N-oxide) resolution. The simplest n-side proton pathway extends from the aqueous phase via Asp20 and Arg207 (cytochrome b6 subunit) to quinone bound axially to heme c(n). On the positive side, the heme-proximal Glu78 (subunit IV), which accepts protons from plastosemiquinone, defines a route for H(+) transfer to the aqueous phase. These pathways provide a structure-based description of the quinone-mediated proton transfer responsible for generation of the transmembrane electrochemical potential gradient in oxygenic photosynthesis.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A384
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4160Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93SX1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f289Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93SW9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit 1179Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.10.9.1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93SX0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 631Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YVQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 734Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3Y1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 537Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58246
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 829Nostoc sp. PCC 7120 = FACHB-418Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61048
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
R [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OPC
Query on OPC

Download Ideal Coordinates CCD File 
S [auth B],
U [auth C]
(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
SQD
Query on SQD

Download Ideal Coordinates CCD File 
X [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
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
T [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
7PH
Query on 7PH

Download Ideal Coordinates CCD File 
V [auth C](1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
BA [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
O [auth A],
Q [auth A],
Z [auth F]
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
8K6
Query on 8K6

Download Ideal Coordinates CCD File 
P [auth A]Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
MYS
Query on MYS

Download Ideal Coordinates CCD File 
N [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
Y [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
AA [auth F]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
W [auth C]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.127α = 90
b = 159.127β = 90
c = 364.373γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 2.0: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description