4PV1

Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.

Hasan, S.S.Proctor, E.A.Yamashita, E.Dokholyan, N.V.Cramer, W.A.

(2014) Biophys J 107: 1620-1628

  • DOI: 10.1016/j.bpj.2014.08.003
  • Primary Citation of Related Structures:  
    4PV1

  • PubMed Abstract: 
  • The cytochrome bc complexes b6f and bc1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Qp portal, 11 Å long in bc complexes ...

    The cytochrome bc complexes b6f and bc1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Qp portal, 11 Å long in bc complexes. Superoxide, which has multiple signaling functions, is a by-product of the p-side quinol oxidation. Although the transmembrane core and the chemistry of quinone redox reactions are conserved in bc complexes, the rate of superoxide generation is an order of magnitude greater in the b6f complex, implying that functionally significant differences in structure exist between the b6f and bc1 complexes on the p-side. A unique structure feature of the b6f p-side quinol oxidation site is the presence of a single chlorophyll-a molecule whose function is unrelated to light harvesting. This study describes a cocrystal structure of the cytochrome b6f complex with the quinol analog stigmatellin, which partitions in the Qp portal of the bc1 complex, but not effectively in b6f. It is inferred that the Qp portal is partially occluded in the b6f complex relative to bc1. Based on a discrete molecular-dynamics analysis, occlusion of the Qp portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Qp portal and is inferred to be a cause of enhanced superoxide production. This study attributes a novel (to our knowledge), structure-linked function to the otherwise enigmatic chlorophyll-a in the b6f complex, which may also be relevant to intracellular redox signaling.


    Organizational Affiliation

    Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, Indiana. Electronic address: waclab@purdue.edu.



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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  • Reference Sequence
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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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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 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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U [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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AA [auth E], V [auth B], Z [auth D](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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Y [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
HEC (Subject of Investigation/LOI)
Query on HEC

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K [auth A], L [auth A], M [auth A], W [auth C]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
7PH (Subject of Investigation/LOI)
Query on 7PH

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Q [auth A](1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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

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P [auth A]STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
UMQ (Subject of Investigation/LOI)
Query on UMQ

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N [auth A], O [auth A], T [auth B]UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
8K6 (Subject of Investigation/LOI)
Query on 8K6

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R [auth B]Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
 Ligand Interaction
MYS (Subject of Investigation/LOI)
Query on MYS

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I [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.085α = 90
b = 159.085β = 90
c = 361.322γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Derived calculations, Refinement description
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary