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 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


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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:  
    4V9G

  • 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. 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Light-harvesting protein B-875 alpha chain58Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufA
UniProt
Find proteins for P0C0X9 (Rhodobacter sphaeroides)
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Go to UniProtKB:  P0C0X9
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXO [auth AB], UA [auth BB]82Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P13402 (Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Light-harvesting protein B-875 beta chain49Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q3J1A3 (Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein H chainDA [auth AH], JB [auth BH]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
UniProt
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein L chainEA [auth AL], KB [auth BL]282Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufL
UniProt
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainFA [auth AM], LB [auth BM]308Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufM
UniProt
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth AZ] , AD [auth BT] , AE [auth BK] , BC [auth AS] , BD [auth BV] , BE [auth BL] , CC [auth A9] , CD [auth BV] , 
AC [auth AZ],  AD [auth BT],  AE [auth BK],  BC [auth AS],  BD [auth BV],  BE [auth BL],  CC [auth A9],  CD [auth BV],  CE [auth BL],  DC [auth AO],  DD [auth B3],  DE [auth BL],  EC [auth A6],  ED [auth B7],  FC [auth A6],  FD [auth BD],  GC [auth AW],  GD [auth BD],  HC [auth AY],  HD [auth BF],  IC [auth AY],  ID [auth BF],  IE [auth BM],  JC [auth A4],  JD [auth B1],  KC [auth A8],  KD [auth B2],  LC [auth AG],  LD [auth BP],  MB [auth AT],  MC [auth AI],  MD [auth BP],  NB [auth AT],  NC [auth AK],  ND [auth BZ],  OB [auth AV],  OC [auth AL],  OD [auth BZ],  PB [auth A3],  PC [auth AL],  PD [auth B9],  QB [auth A7],  QD [auth BO],  RB [auth AD],  RD [auth BO],  SB [auth AD],  SD [auth B6],  TB [auth AF],  TC [auth AM],  TD [auth BU],  UB [auth A1],  UC [auth AM],  UD [auth BY],  VB [auth AJ],  VD [auth BY],  WB [auth A2],  WD [auth B4],  XB [auth AN],  XD [auth B8],  YB [auth AP],  YD [auth BI],  ZB [auth AP],  ZC [auth B5],  ZD [auth BK]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH (Subject of Investigation/LOI)
Query on BPH

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EE [auth BL], JE [auth BM], QC [auth AL], VC [auth AM]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10 (Subject of Investigation/LOI)
Query on U10

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GE [auth BL], RC [auth AL], XC [auth AM]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SPO (Subject of Investigation/LOI)
Query on SPO

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YC [auth AM]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
PO4
Query on PO4

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HE [auth BL], SC [auth AL]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE2
Query on FE2

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FE [auth BL], WC [auth AM]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-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 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.077α = 90
b = 415.075β = 105.75
c = 129.818γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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