4H44 | pdb_00004h44

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 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 116.45 kDa 
  • Atom Count: 8,128 
  • Modeled Residue Count: 959 
  • Deposited Residue Count: 974 
  • Unique protein chains: 8

Macromolecules

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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
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UniProt GroupP0A384
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Reference Sequence
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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
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UniProt GroupQ93SX1
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Reference Sequence
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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))
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Reference Sequence
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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 (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))
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Go to UniProtKB:  Q93SX0
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UniProt GroupQ93SX0
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Reference Sequence
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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))
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Go to UniProtKB:  Q8YVQ2
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Reference Sequence
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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
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Reference Sequence
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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
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UniProt GroupP58246
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Reference Sequence
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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
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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 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
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

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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
  • Version 2.1: 2024-11-20
    Changes: Structure summary