4RCR

STRUCTURE OF THE REACTION CENTER FROM RHODOBACTER SPHAEROIDES R-26 AND 2.4.1: PROTEIN-COFACTOR (BACTERIOCHLOROPHYLL, BACTERIOPHEOPHYTIN, AND CAROTENOID) INTERACTIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions.

Yeates, T.O.Komiya, H.Chirino, A.Rees, D.C.Allen, J.P.Feher, G.

(1988) Proc Natl Acad Sci U S A 85: 7993-7997

  • DOI: 10.1073/pnas.85.21.7993
  • Primary Citation of Related Structures:  
    4RCR

  • PubMed Abstract: 
  • The three-dimensional structures of the cofactors and protein subunits of the reaction center (RC) from the carotenoidless mutant strain of Rhodobacter sphaeroides R-26 and the wild-type strain 2.4.1 have been determined by x-ray diffraction to resolutions of 2 ...

    The three-dimensional structures of the cofactors and protein subunits of the reaction center (RC) from the carotenoidless mutant strain of Rhodobacter sphaeroides R-26 and the wild-type strain 2.4.1 have been determined by x-ray diffraction to resolutions of 2.8 A and 3.0 A with R values of 24% and 26%, respectively. The bacteriochlorophyll dimer (D), bacteriochlorophyll monomers (B), and bacteriopheophytin monomers (phi) form two branches, A and B, that are approximately related by a twofold symmetry axis. The cofactors are located in hydrophobic environments formed by the L and M subunits. Differences in the cofactor-protein interactions between the A and B cofactors, as well as between the corresponding cofactors of Rb, sphaeroides and Rhodopseudomonas viridis [Michel, H., Epp, O. & Deisenhofer, J. (1986) EMBO J. 3, 2445-2451], are delineated. The roles of several structural features in the preferential electron transfer along the A branch are discussed. Two bound detergent molecules of beta-octyl glucoside have been located near BA and BB. The environment of the carotenoid, C, that is present in RCs from Rb. sphaeroides 2.4.1 consists largely of aromatic residues of the M subunit. A role of BB in the triplet energy transfer from D to C and the reason for the preferential ease of removal of BB from the RC is proposed.


    Related Citations: 
    • Structure and Function of Bacterial Photosynthetic Reaction Centres
      Feher, G., Allen, J.P., Okamura, M.Y., Rees, D.C.
      (1989) Nature 339: 111
    • The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins
      Rees, D.C., Komiya, H., Yeates, T.O., Allen, J.P., Feher, G.
      (1989) Annu Rev Biochem 58: 607
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1: Symmetry Relations and Sequence Comparisons between Different Species
      Komiya, H., Yeates, T.O., Rees, D.C., Allen, J.P., Feher, G.
      (1988) Proc Natl Acad Sci U S A 85: 9012
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Protein-Cofactor (Quinones and Fe2+) Interactions
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1988) Proc Natl Acad Sci U S A 85: 8487
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Protein Subunits
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1987) Proc Natl Acad Sci U S A 84: 6162
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Cofactors
      Allen, J.P., Feher, G., Yeates, T.O., Komiya, H., Rees, D.C.
      (1987) Proc Natl Acad Sci U S A 84: 5730
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Membrane-Protein Interactions
      Yeates, T.O., Komiya, H., Rees, D.C., Allen, J.P., Feher, G.
      (1987) Proc Natl Acad Sci U S A 84: 6438
    • Structural Homology of Reaction Centers from Rhodopseudomonas Sphaeroides and Rhodopseudomonas Viridis as Determined by X-Ray Diffraction
      Allen, J.P., Feher, G., Yeates, T.O., Rees, D.C., Deisenhofer, J., Michel, H., Huber, R.
      (1986) Proc Natl Acad Sci U S A 83: 8589
    • Crystallization of Reaction Center from Rhodopseudomonas Sphaeroides: Preliminary Characterization
      Allen, J.P., Feher, G.
      (1984) Proc Natl Acad Sci U S A 81: 4795

    Organizational Affiliation

    University of California, Los Angeles 90024.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERA [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERB [auth M]307Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
D [auth L], E [auth L], J [auth M], K [auth M]BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH (Subject of Investigation/LOI)
Query on BPH

Download Ideal Coordinates CCD File 
F [auth L], L [auth M]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
G [auth L], MUBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
H [auth M]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
I [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 77.5β = 90
c = 141.8γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary