4H0L

Cytochrome b6f Complex Crystal Structure from Mastigocladus laminosus with n-Side Inhibitor NQNO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1073/pnas.1222248110
  • Primary Citation of Related Structures:  
    4H44, 4H0L, 4H13

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6A215Mastigocladus laminosusMutation(s): 0 
Gene Names: petB
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4B160Mastigocladus laminosusMutation(s): 0 
Gene Names: petD
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Apocytochrome fC289Mastigocladus laminosusMutation(s): 0 
Gene Names: petA
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunitD179Mastigocladus laminosusMutation(s): 0 
Gene Names: petC
EC: 1.10.9.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6E32Mastigocladus laminosusMutation(s): 0 
Gene Names: petL
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7F35Mastigocladus laminosusMutation(s): 0 
Gene Names: petM
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5G37Mastigocladus laminosusMutation(s): 0 
Gene Names: petG
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8H29Mastigocladus laminosusMutation(s): 0 
Gene Names: petN
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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S [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
OPC (Subject of Investigation/LOI)
Query on OPC

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M [auth A], T [auth B](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
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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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
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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J [auth A], K [auth A], L [auth A], V [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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Y [auth G]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
UMQ (Subject of Investigation/LOI)
Query on UMQ

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N [auth A], O [auth A], Q [auth A], U [auth C]UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
QNO (Subject of Investigation/LOI)
Query on QNO

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P [auth A]2-NONYL-4-HYDROXYQUINOLINE N-OXIDE
C18 H25 N O2
LMBFBUICIQJLPK-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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W [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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I [auth A], R [auth B]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.133α = 90
b = 159.133β = 90
c = 362.25γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
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: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references