4V9G

RC-LH1-PufX dimer complex from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.78 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX.

Qian, P.Papiz, M.Z.Jackson, P.J.Brindley, A.A.Ng, I.W.Olsen, J.D.Dickman, M.J.Bullough, P.A.Hunter, C.N.

(2013) Biochemistry 52: 7575-7585

  • DOI: 10.1021/bi4011946
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Reaction center-light harvesting 1 (RC-LH1) complexes are the fundamental units of bacterial photosynthesis, which use solar energy to power the reduction of quinone to quinol prior to the formation of the proton gradient that drives ATP synthesis. T ...

    Reaction center-light harvesting 1 (RC-LH1) complexes are the fundamental units of bacterial photosynthesis, which use solar energy to power the reduction of quinone to quinol prior to the formation of the proton gradient that drives ATP synthesis. The dimeric RC-LH1-PufX complex of Rhodobacter sphaeroides is composed of 64 polypeptides and 128 cofactors, including 56 LH1 bacteriochlorophyll a (BChl a) molecules that surround and donate energy to the two RCs. The 3D structure was determined to 8 Å by X-ray crystallography, and a model was built with constraints provided by electron microscopy (EM), nuclear magnetic resonance (NMR), mass spectrometry (MS), and site-directed mutagenesis. Each half of the dimer complex consists of a RC surrounded by an array of 14 LH1 αβ subunits, with two BChls sandwiched between each αβ pair of transmembrane helices. The N- and C-terminal extrinsic domains of PufX promote dimerization by interacting with the corresponding domains of an LH1 β polypeptide from the other half of the RC-LH1-PufX complex. Close contacts between PufX, an LH1 αβ subunit, and the cytoplasmic domain of the RC-H subunit prevent the LH1 complex from encircling the RC and create a channel connecting the RC QB site to an opening in the LH1 ring, allowing Q/QH₂ exchange with the external quinone pool. We also identified a channel that connects the two halves of the dimer, potentially forming a long-range pathway for quinone migration along rows of RC-LH1-PufX complexes in the membrane. The structure of the RC-LH1-PufX complex explains the crucial role played by PufX in dimer formation, and it shows how quinone traffic traverses the LH1 complex as it shuttles between the RC and the cytochrome bc₁ complex.


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield , Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light-harvesting protein B-875 alpha chain
A5, AT, AV, AX, A3, A7, AD, AF, A1, AJ, A2, AN, AP, AZ, B5, BT, BV, BX, B3, B7, BD, BF, B1, BJ, B2, BN, BP, BZ
58Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufA
Find proteins for P0C0X9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0X9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Intrinsic membrane protein PufX
AB, BB
82Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Mutation(s): 0 
Gene Names: pufX
Find proteins for P13402 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  P13402
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light-harvesting protein B-875 beta chain
AS, A9, AO, AQ, A6, AU, AW, AY, A4, A8, AE, AG, AI, AK, BS, B9, BO, BQ, B6, BU, BW, BY, B4, B8, BE, BG, BI, BK
49Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Mutation(s): 0 
Gene Names: pufB
Find proteins for Q3J1A3 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q3J1A3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chain
AH, BH
260Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein L chain
AL, BL
282Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein M chain
AM, BM
308Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
AL, BL
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
U10
Query on U10

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Download CCD File 
AL, AM, BL
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
BCL
Query on BCL

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Download CCD File 
A1, A2, A3, A4, A6, A7, A8, A9, AD, AF, AG, AI, AJ, AK, AL, AM, AN, AO, AP, AS, AT, AV, AW, AY, AZ, B1, B2, B3, B4, B5, B6, B7, B8, B9, BD, BF, BI, BK, BL, BM, BO, BP, BT, BU, BV, BY, BZ
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
AM, BL
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPH
Query on BPH

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Download CCD File 
AL, AM, BL, BM
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
SPO
Query on SPO

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Download CCD File 
AM
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.78 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.077α = 90.00
b = 415.075β = 105.75
c = 129.818γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
GDAdata collection
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other