1IJD

Crystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.243 

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This is version 1.4 of the entry. See complete history


Literature

The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050.

McLuskey, K.Prince, S.M.Cogdell, R.J.Isaacs, N.W.

(2001) Biochemistry 40: 8783-8789

  • DOI: https://doi.org/10.1021/bi010309a
  • Primary Citation of Related Structures:  
    1IJD

  • PubMed Abstract: 

    The B800-820, or LH3, complex is a spectroscopic variant of the B800-850 LH2 peripheral light-harvesting complex. LH3 is synthesized by some species and strains of purple bacteria when growing under what are generally classed as "stressed" conditions, such as low intensity illumination and/or low temperature (<30 degrees C). The apoproteins in these complexes modify the absorption properties of the chromophores to ensure that the photosynthetic process is highly efficient. The crystal structure of the B800-820 light-harvesting complex, an integral membrane pigment-protein complex, from the purple bacteria Rhodopseudomonas (Rps.) acidophila strain 7050 has been determined to a resolution of 3.0 A by molecular replacement. The overall structure of the LH3 complex is analogous to that of the LH2 complex from Rps. acidophila strain 10050. LH3 has a nonameric quaternary structure where two concentric cylinders of alpha-helices enclose the pigment molecules bacteriochlorophyll a and carotenoid. The observed spectroscopic differences between LH2 and LH3 can be attributed to differences in the primary structure of the apoproteins. There are changes in hydrogen bonding patterns between the coupled Bchla molecules and the protein that have an effect on the conformation of the C3-acetyl groups of the B820 molecules. The structure of LH3 shows the important role that the protein plays in modulating the characteristics of the light-harvesting system and indicates the mechanisms by which the absorption properties of the complex are altered to produce a more efficient light-harvesting component.


  • Organizational Affiliation

    Department of Chemistry, Division of Biochemistry and Molecular Biology IBLS, University of Glasgow, Glasgow, Scotland G12 8QQ, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
A, C, E
53Rhodoblastus acidophilusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P35089 (Rhodoblastus acidophilus)
Explore P35089 
Go to UniProtKB:  P35089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35089
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
B, D, F
42Rhodoblastus acidophilusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P35094 (Rhodoblastus acidophilus)
Explore P35094 
Go to UniProtKB:  P35094
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35094
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth C]
M [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth E],
R [auth E],
U [auth F]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
RPA
Query on RPA

Download Ideal Coordinates CCD File 
I [auth B],
N [auth D],
S [auth F]
RHODOPINAL GLUCOSIDE
C46 H66 O7
KKQLCQBTEUVHBX-DSGXVNCLSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
J [auth B],
O [auth D],
T [auth F]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, C, E
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.243 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.26α = 90
b = 117.26β = 90
c = 295.92γ = 120
Software Package:
Software NamePurpose
AMoREphasing
RESTRAINrefinement
MOSFLMdata reduction
CCP4data 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: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary