4V8K | pdb_00004v8k

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in P21 form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.356 (Depositor), 0.344 (DCC) 
  • R-Value Work: 
    0.335 (Depositor), 0.342 (DCC) 
  • R-Value Observed: 
    0.336 (Depositor) 

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This is version 1.3 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: https://doi.org/10.1038/nature13197
  • Primary Citation 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 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: 
    • 1] Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan [2].

Macromolecule Content 

  • Total Structure Weight: 785.24 kDa 
  • Atom Count: 50,862 
  • Modeled Residue Count: 5,429 
  • Deposited Residue Count: 5,994 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth AC],
KA [auth BC]		404Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P5 (Thermochromatium tepidum)
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Entity Groups
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UniProt GroupD2Z0P5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitB [auth AL],
LA [auth BL]		281Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P3 (Thermochromatium tepidum)
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Entity Groups
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UniProt GroupD2Z0P3
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitC [auth AM],
MA [auth BM]		325Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8ASG6 (Thermochromatium tepidum)
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UniProt GroupA8ASG6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth AH],
NA [auth BH]		259Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P9 (Thermochromatium tepidum)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
LH1 alpha polypeptide61Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum)
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL

Query on BCL


Download:Ideal Coordinates CCD File
AE [auth AV]
AF [auth A9]
AG [auth BD]
AH [auth BT]
BE [auth AW]
AE [auth AV],
AF [auth A9],
AG [auth BD],
AH [auth BT],
BE [auth AW],
BG [auth BE],
BI [auth B7],
CC [auth AL],
CD [auth AI],
CF [auth A0],
CH [auth BU],
CI [auth B8],
DC [auth AM],
DD [auth AJ],
DE [auth AX],
DG [auth BF],
EC [auth AM],
EH [auth BV],
EI [auth B9],
FG [auth BG],
GD [auth AK],
GE [auth AY],
GI [auth B0],
HD [auth AN],
HE [auth AZ],
HH [auth BW],
IF [auth BL],
IG [auth BI],
JE [auth A1],
JG [auth BJ],
JH [auth BX],
KD [auth AO],
LD [auth AP],
LE [auth A2],
LF [auth BL],
LG [auth BK],
LH [auth BY],
MF [auth BM],
MG [auth BN],
MH [auth BZ],
NF [auth BM],
OD [auth AQ],
OH [auth B1],
PC [auth AA],
PD [auth AR],
PE [auth A3],
PG [auth BO],
QE [auth A3],
QH [auth B2],
RG [auth BP],
SC [auth AB],
SE [auth A5],
TD [auth AS],
TH [auth B3],
UE [auth A6],
UF [auth BA],
UH [auth B4],
VC [auth AD],
VD [auth AT],
VG [auth BQ],
WC [auth AE],
WG [auth BQ],
WH [auth B5],
XE [auth A7],
XF [auth BB],
YC [auth AF],
YD [auth AU],
YE [auth A8],
YG [auth BS],
YH [auth B6],
ZB [auth AL],
ZC [auth AG]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH


Download:Ideal Coordinates CCD File
AC [auth AL],
FC [auth AM],
JF [auth BL],
OF [auth BM]		BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
UQ8

Query on UQ8


Download:Ideal Coordinates CCD File
BC [auth AL],
KF [auth BL]		Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ8

Query on MQ8


Download:Ideal Coordinates CCD File
HC [auth AM],
QF [auth BM]		MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF

Query on PEF


Download:Ideal Coordinates CCD File
JC [auth AM]
KC [auth AM]
LC [auth AM]
NC [auth AH]
RD [auth AS]
JC [auth AM],
KC [auth AM],
LC [auth AM],
NC [auth AH],
RD [auth AS],
SF [auth BM],
TG [auth BQ]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEM

Query on HEM


Download:Ideal Coordinates CCD File
DF [auth BC]
EF [auth BC]
FF [auth BC]
GF [auth BC]
UB [auth AC]
DF [auth BC],
EF [auth BC],
FF [auth BC],
GF [auth BC],
UB [auth AC],
VB [auth AC],
WB [auth AC],
XB [auth AC]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CRT

Query on CRT


Download:Ideal Coordinates CCD File
AD [auth AG]
AI [auth B7]
BF [auth A0]
CE [auth AW]
DH [auth BU]
AD [auth AG],
AI [auth B7],
BF [auth A0],
CE [auth AW],
DH [auth BU],
ED [auth AJ],
EE [auth AX],
EG [auth BF],
FH [auth BV],
FI [auth B0],
GG [auth BG],
IC [auth AM],
ID [auth AN],
IH [auth BW],
KE [auth A1],
MD [auth AP],
ME [auth A2],
NG [auth BN],
PH [auth B1],
QC [auth AA],
QD [auth AR],
QG [auth BO],
RF [auth BM],
RH [auth B2],
SG [auth BP],
TC [auth AB],
TE [auth A5],
UD [auth AS],
VF [auth BA],
WD [auth AT],
WE [auth A7],
XH [auth B5],
YF [auth BB],
ZG [auth BS]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
MC [auth AM],
NE [auth A3],
OC [auth AH],
TF [auth BH]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE

Query on FE


Download:Ideal Coordinates CCD File
GC [auth AM],
PF [auth BM]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
BD [auth AI]
BH [auth BU]
CG [auth BF]
DI [auth B9]
FD [auth AK]
BD [auth AI],
BH [auth BU],
CG [auth BF],
DI [auth B9],
FD [auth AK],
FE [auth AY],
GH [auth BW],
HF [auth BC],
HG [auth BI],
IE [auth A1],
JD [auth AO],
KG [auth BK],
KH [auth BY],
ND [auth AQ],
NH [auth B1],
OE [auth A3],
OG [auth BO],
RC [auth AA],
RE [auth A5],
SD [auth AS],
SH [auth B3],
UC [auth AD],
UG [auth BQ],
VE [auth A7],
VH [auth B5],
WF [auth BA],
XC [auth AF],
XD [auth AU],
XG [auth BS],
YB [auth AC],
ZD [auth AV],
ZE [auth A9],
ZF [auth BD],
ZH [auth B7]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free:  0.356 (Depositor), 0.344 (DCC) 
  • R-Value Work:  0.335 (Depositor), 0.342 (DCC) 
  • R-Value Observed: 0.336 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.159α = 90
b = 145.429β = 108.5
c = 210.528γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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
  • Version 1.2: 2017-06-07
    Changes: Other
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Structure summary