9J2F

Structure of photosynthetic LH1-RC complex from the purple bacterium Blastochloris tepida


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The thermal-stable LH1-RC complex of a hot spring purple bacterium powers photosynthesis with extremely low-energy near-infrared light.

Kimura, Y.Kanno, R.Mori, K.Matsuda, Y.Seto, R.Takenaka, S.Mino, H.Ohkubo, T.Honda, M.Sasaki, Y.C.Kishikawa, J.Mitsuoka, K.Mio, K.Hall, M.Purba, E.R.Mochizuki, T.Mizoguchi, A.Humbel, B.M.Madigan, M.T.Wang-Otomo, Z.-Y.Tani, K.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]354Blastochloris tepidaMutation(s): 0 
UniProt
Find proteins for A0A348FW74 (Blastochloris tepida)
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UniProt GroupA0A348FW74
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]274Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348FW72 (Blastochloris tepida)
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UniProt GroupA0A348FW72
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]332Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A348FW73
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center subunit HD [auth H]260Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348FW44 (Blastochloris tepida)
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UniProt GroupA0A348FW44
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing protein69Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348FW71 (Blastochloris tepida)
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UniProt GroupA0A348FW71
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing protein69Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348FW70 (Blastochloris tepida)
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UniProt GroupA0A348FW70
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein gamma156Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348G0X9 (Blastochloris tepida)
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UniProt GroupA0A348G0X9
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-1015 gamma chain57Blastochloris tepidaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A348G0Y0 (Blastochloris tepida)
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UniProt GroupA0A348G0Y0
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AC [auth H],
ME [auth r],
NB [auth L],
WB [auth M],
ZB [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCB (Subject of Investigation/LOI)
Query on BCB

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AD [auth W]
BE [auth k]
CC [auth A]
DD [auth X]
ED [auth Z]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB
Query on BPB

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LB [auth L],
RB [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
PGV
Query on PGV

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HC [auth D]
LC [auth I]
OC [auth N]
RC [auth Q]
YB [auth M]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
UQ8
Query on UQ8

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BC [auth A],
HB [auth C],
MB [auth L],
UB [auth M],
VB [auth M]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ7
Query on MQ7

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SB [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
DGA
Query on DGA

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IB [auth L]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC
Query on HEC

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CB [auth C],
DB [auth C],
EB [auth C],
FB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NS0
Query on NS0

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AE [auth k]
BD [auth W]
CD [auth X]
DC [auth A]
DE [auth l]
all-trans-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-XILUKMICSA-N
NS5
Query on NS5

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TB [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
LMT
Query on LMT

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CE [auth k]
EC [auth B]
GE [auth n]
RD [auth b]
SD [auth b]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

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OB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

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GB [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
D [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101118
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101116
Japan Society for the Promotion of Science (JSPS)JapanJP16H04174
Japan Society for the Promotion of Science (JSPS)JapanJP18H05153
Japan Society for the Promotion of Science (JSPS)Japan20H05086
Japan Society for the Promotion of Science (JSPS)Japan20H02856

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release