1LGH

CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM RHODOSPIRILLUM MOLISCHIANUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

Starting Model: in silico
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This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum.

Koepke, J.Hu, X.Muenke, C.Schulten, K.Michel, H.

(1996) Structure 4: 581-597

  • DOI: https://doi.org/10.1016/s0969-2126(96)00063-9
  • Primary Citation of Related Structures:  
    1LGH

  • PubMed Abstract: 

    The light-harvesting complexes II (LH-2s) are integral membrane proteins that form ring-like structures, oligomers of alpha beta-heterodimers, in the photosynthetic membranes of purple bacteria. They contain a large number of chromophores organized optimally for light absorption and rapid light energy migration. Recently, the structure of the nonameric LH-2 of Rhodopseudomonas acidophila has been determined; we report here the crystal structure of the octameric LH-2 from Rhodospirillum molischianum. The unveiling of similarities and differences in the architecture of these proteins may provide valuable insight into the efficient energy transfer mechanisms of bacterial photosynthesis. The crystal structure of LH-2 from Rs. molischianum has been determined by molecular replacement at 2.4 A resolution using X-ray diffraction. The crystal structure displays two concentric cylinders of sixteen membrane-spanning helical subunits, containing two rings of bacteriochlorophyll-a (BChl-a) molecules. One ring comprises sixteen B850 BChl-as perpendicular to the membrane plane and the other eight B800 BChl-as that are nearly parallel to the membrane plane; eight membrane-spanning lycopenes (the major carotenoid in this complex) stretch out between the B800 and B850 BChl-as. The B800 BChl-as exhibit a different ligation from that of Rps. acidophila (aspartate is the Mg ligand as opposed to formyl-methionine in Rps. acidophila). The light-harvesting complexes from different bacteria assume various ring sizes. In LH-2 of Rs. molischianum, the Qy transition dipole moments of neighbouring B850 and B800 BChl-as are nearly parallel to each other, that is, they are optimally aligned for Föster exciton transfer. Dexter energy transfer between these chlorophylls is also possible through interactions mediated by lycopenes and B850 BChl-a phytyl tails; the B800 BChl-a and one of the two B850 BChl-as associated with each heterodimeric unit are in van der Waals distance to a lycopene, such that singlet and triplet energy transfer between lycopene and the BChl-as can occur by the Dexter mechanism. The ring structure of the B850 BChl-as is optimal for light energy transfer in that it samples all spatial absorption and emission characteristics and places all oscillator strength into energetically low lying, thermally accessible exciton states.


  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Molekulare Membranbiologie, Frankfurt, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIGHT HARVESTING COMPLEX IIA,
C [auth D],
E [auth G],
G [auth J]
56Magnetospirillum molischianumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P97253 (Magnetospirillum molischianum)
Explore P97253 
Go to UniProtKB:  P97253
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97253
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LIGHT HARVESTING COMPLEX IIB,
D [auth E],
F [auth H],
H [auth K]
45Magnetospirillum molischianumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P95673 (Magnetospirillum molischianum)
Explore P95673 
Go to UniProtKB:  P95673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95673
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download Ideal Coordinates CCD File 
DB [auth K]
EA [auth E]
I [auth A]
J [auth A]
JA [auth G]
DB [auth K],
EA [auth E],
I [auth A],
J [auth A],
JA [auth G],
KA [auth G],
O [auth B],
PA [auth H],
U [auth D],
V [auth D],
VA [auth J],
WA [auth J]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
LYC
Query on LYC

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K [auth A],
LA [auth G],
W [auth D],
XA [auth J]
LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
DET
Query on DET

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EB [auth K]
FA [auth E]
FB [auth K]
GA [auth E]
L [auth A]
EB [auth K],
FA [auth E],
FB [auth K],
GA [auth E],
L [auth A],
MA [auth G],
P [auth B],
Q [auth B],
QA [auth H],
RA [auth H],
X [auth D],
YA [auth J]
UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
C13 H29 N O
OZHBUVQCJMARBN-UHFFFAOYSA-N
HTO
Query on HTO

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AA [auth D]
AB [auth J]
BA [auth D]
BB [auth J]
CA [auth D]
AA [auth D],
AB [auth J],
BA [auth D],
BB [auth J],
CA [auth D],
CB [auth K],
DA [auth E],
GB [auth K],
HA [auth E],
HB [auth K],
IA [auth E],
M [auth A],
N [auth A],
NA [auth G],
OA [auth G],
R [auth B],
S [auth D],
SA [auth H],
T [auth D],
TA [auth J],
UA [auth J],
Y [auth D],
Z [auth D],
ZA [auth J]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.6α = 90
b = 91.6β = 90
c = 209.97γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-05
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description