3WMM

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in C2 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.315 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom

Niwa, S.Yu, L.J.Takeda, K.Hirano, Y.Kawakami, T.Wang-Otomo, Z.Y.Miki, K.

(2014) Nature 508: 228-232

  • DOI: 10.1038/nature13197
  • Primary Citation of Related Structures:  
    3WMM, 4V8K

  • PubMed Abstract: 
  • The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1-RC) to use sunlight energy in a highly efficient manner. Here we report the first near-atomic structure, to our knowledge, of a LH1-RC complex, namely that of a Ca(2+)-bound complex from Thermochromatium tepidum, which reveals detailed information on the arrangement and interactions of the protein subunits and the cofactors ...

    The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1-RC) to use sunlight energy in a highly efficient manner. Here we report the first near-atomic structure, to our knowledge, of a LH1-RC complex, namely that of a Ca(2+)-bound complex from Thermochromatium tepidum, which reveals detailed information on the arrangement and interactions of the protein subunits and the cofactors. The RC is surrounded by 16 heterodimers of the LH1 αβ-subunit that form a completely closed structure. The Ca(2+) ions are located at the periplasmic side of LH1. Thirty-two bacteriochlorophyll and 16 spirilloxanthin molecules in the LH1 ring form an elliptical assembly. The geometries of the pigment assembly involved in the absorption characteristics of the bacteriochlorophyll in LH1 and excitation energy transfer among the pigments are reported. In addition, possible ubiquinone channels in the closed LH1 complex are proposed based on the atomic structure.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center C subunitA [auth C]404Thermochromatium tepidumMutation(s): 0 
Gene Names: pufC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P5 (Thermochromatium tepidum)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitB [auth L]281Thermochromatium tepidumMutation(s): 0 
Gene Names: pufL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P3 (Thermochromatium tepidum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitC [auth M]325Thermochromatium tepidumMutation(s): 0 
Gene Names: pufM
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for A8ASG6 (Thermochromatium tepidum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]259Thermochromatium tepidumMutation(s): 0 
Gene Names: puhA
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P9 (Thermochromatium tepidum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
LH1 alpha polypeptide61Thermochromatium tepidumMutation(s): 0 
Gene Names: pufA
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P2 (Thermochromatium tepidum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Gene Names: pufB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P1 (Thermochromatium tepidum)
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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AD [auth 1] , BD [auth 2] , CC [auth O] , DC [auth P] , ED [auth 3] , GC [auth Q] , GD [auth 4] , HB [auth A] , 
AD [auth 1],  BD [auth 2],  CC [auth O],  DC [auth P],  ED [auth 3],  GC [auth Q],  GD [auth 4],  HB [auth A],  HC [auth R],  JD [auth 5],  KB [auth B],  KC [auth S],  KD [auth 6],  LC [auth T],  MD [auth 7],  NB [auth D],  ND [auth 7],  OB [auth E],  OC [auth U],  PA [auth L],  PC [auth V],  QB [auth F],  QD [auth 9],  RB [auth G],  RD [auth 0],  SC [auth W],  TA [auth L],  UA [auth M],  UB [auth I],  UC [auth X],  VA [auth M],  VB [auth I],  XC [auth Y],  YB [auth K],  YC [auth Z],  ZB [auth N]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

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QA [auth L], WA [auth M]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
PGW
Query on PGW

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AB [auth M], DB [auth H](1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
 Ligand Interaction
UQ8
Query on UQ8

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RA [auth L]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
 Ligand Interaction
MQ8
Query on MQ8

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YA [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
 Ligand Interaction
PEF
Query on PEF

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CB [auth H]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
HEM
Query on HEM

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KA [auth C], LA [auth C], MA [auth C], NA [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CRT
Query on CRT

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AC [auth N] , CD [auth 2] , EC [auth P] , FD [auth 3] , GB [auth A] , HD [auth 4] , IB [auth A] , IC [auth R] , 
AC [auth N],  CD [auth 2],  EC [auth P],  FD [auth 3],  GB [auth A],  HD [auth 4],  IB [auth A],  IC [auth R],  LB [auth B],  MC [auth T],  OD [auth 8],  QC [auth V],  SB [auth G],  TC [auth W],  VC [auth X],  WB [auth J],  ZA [auth M]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
 Ligand Interaction
PO4
Query on PO4

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BB [auth M], EB [auth H], FB [auth H], SA [auth L]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

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XA [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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BC [auth O] , DD [auth 3] , FC [auth Q] , ID [auth 5] , JB [auth A] , JC [auth S] , LD [auth 7] , MB [auth D] , 
BC [auth O],  DD [auth 3],  FC [auth Q],  ID [auth 5],  JB [auth A],  JC [auth S],  LD [auth 7],  MB [auth D],  NC [auth U],  OA [auth C],  PB [auth F],  PD [auth 9],  RC [auth W],  TB [auth I],  WC [auth Y],  XB [auth K],  ZC [auth 1]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.315 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.341α = 90
b = 148.238β = 117.59
c = 161.792γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Other