7VRJ | pdb_00007vrj

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7VRJ

This is version 1.2 of the entry. See complete history

Literature

A Ca 2+ -binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.

Tani, K.Kobayashi, K.Hosogi, N.Ji, X.C.Nagashima, S.Nagashima, K.V.P.Izumida, A.Inoue, K.Tsukatani, Y.Kanno, R.Hall, M.Yu, L.J.Ishikawa, I.Okura, Y.Madigan, M.T.Mizoguchi, A.Humbel, B.M.Kimura, Y.Wang-Otomo, Z.Y.

(2022) J Biological Chem 298: 101967-101967

  • DOI: https://doi.org/10.1016/j.jbc.2022.101967
  • Primary Citation Related Structures: 
    7VRJ

  • PubMed Abstract: 

    The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca 2+ -dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center-associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca 2+ along with β1- or β3-polypeptides to form the Ca 2+ -binding sites. This structure differs from that of fully Ca 2+ -bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca 2+ -binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca 2+ -binding WxxDxI motif that is conserved in all Ca 2+ -bound LH1 α-polypeptides from other species with reported structures. The partial Ca 2+ -bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca 2+ -requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a "transitional" species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits.


  • Organizational Affiliation
    • Graduate School of Medicine, Mie University, Tsu, Japan. Electronic address: ktani@doc.medic.mie-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 404.88 kDa 
  • Atom Count: 26,309 
  • Modeled Residue Count: 2,604 
  • Deposited Residue Count: 2,854 
  • Unique protein chains: 9

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]405Allochromatium tepidumMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitB [auth L]277Allochromatium tepidumMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitC [auth M]324Allochromatium tepidumMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]259Allochromatium tepidumMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 alpha244Allochromatium tepidumMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 beta146Allochromatium tepidumMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 alpha164Allochromatium tepidumMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 beta347Allochromatium tepidumMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 alpha3CA [auth 3]67Allochromatium tepidumMutation(s): 0 

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
BB [auth L]
ED [auth S]
JC [auth I]
LB [auth M]
NB [auth M]
BB [auth L],
ED [auth S],
JC [auth I],
LB [auth M],
NB [auth M],
PB [auth H],
QB [auth H],
YB [auth D]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
(Subject of Investigation/LOI)

Query on BCL



Download:Ideal Coordinates CCD File
AB [auth L]
AD [auth Q]
BE [auth 2]
CC [auth E]
CD [auth R]
AB [auth L],
AD [auth Q],
BE [auth 2],
CC [auth E],
CD [auth R],
DE [auth 3],
EC [auth F],
FB [auth M],
FD [auth S],
FE [auth 4],
HC [auth G],
JD [auth T],
JE [auth 5],
KC [auth I],
KD [auth U],
KE [auth 6],
MC [auth J],
ME [auth 7],
ND [auth V],
OD [auth W],
PE [auth 8],
RC [auth K],
RD [auth X],
RE [auth 9],
SC [auth N],
TA [auth L],
TB [auth A],
TD [auth Y],
TE [auth 0],
VB [auth B],
WC [auth O],
WD [auth Z],
XC [auth P],
ZA [auth L],
ZB [auth D],
ZD [auth 1]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
GB [auth M],
UA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
CB [auth L]
IE [auth 5]
KB [auth M]
MB [auth M]
OB [auth M]
CB [auth L],
IE [auth 5],
KB [auth M],
MB [auth M],
OB [auth M],
RA [auth C],
RB [auth H],
SA [auth L],
XA [auth L],
XB [auth D],
XD [auth 1],
YA [auth L]
(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



Download:Ideal Coordinates CCD File
DB [auth L],
VA [auth L],
WA [auth L]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ8

Query on MQ8



Download:Ideal Coordinates CCD File
HB [auth M],
JB [auth M]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
DGA

Query on DGA



Download:Ideal Coordinates CCD File
PA [auth C]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CRT

Query on CRT



Download:Ideal Coordinates CCD File
BD [auth Q]
CE [auth 2]
DC [auth E]
DD [auth R]
GE [auth 4]
BD [auth Q],
CE [auth 2],
DC [auth E],
DD [auth R],
GE [auth 4],
HD [auth S],
IB [auth M],
IC [auth G],
LE [auth 6],
NC [auth J],
NE [auth 7],
QE [auth 8],
SD [auth X],
TC [auth N],
WB [auth B],
YC [auth P],
YD [auth 1]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AE [auth 2]
BC [auth E]
EE [auth 4]
GC [auth G]
HE [auth 4]
AE [auth 2],
BC [auth E],
EE [auth 4],
GC [auth G],
HE [auth 4],
ID [auth T],
LC [auth J],
MD [auth V],
OC [auth J],
OE [auth 8],
QC [auth K],
QD [auth X],
SB [auth H],
SE [auth 0],
UB [auth B],
UC [auth N],
VD [auth Z],
ZC [auth P]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
QA [auth C]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
PC [auth K],
VC [auth O]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
EB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AC [auth D]
FC [auth F]
GD [auth S]
LD [auth U]
PD [auth W]
AC [auth D],
FC [auth F],
GD [auth S],
LD [auth U],
PD [auth W],
UD [auth Y]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
OA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
AA [auth 1]
E [auth A]
EA [auth 5]
GA [auth 7]
IA [auth 9]
AA [auth 1],
E [auth A],
EA [auth 5],
GA [auth 7],
IA [auth 9],
K [auth I],
M [auth K],
O,
Q
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

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: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary