7VY2 | pdb_00007vy2

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history

Literature

Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.

Tani, K.Kanno, R.Kikuchi, R.Kawamura, S.Nagashima, K.V.P.Hall, M.Takahashi, A.Yu, L.J.Kimura, Y.Madigan, M.T.Mizoguchi, A.Humbel, B.M.Wang-Otomo, Z.Y.

(2022) Nat Commun 13: 1904-1904

  • DOI: https://doi.org/10.1038/s41467-022-29453-8
  • Primary Citation Related Structures: 
    7VY2, 7VY3

  • PubMed Abstract: 

    Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex.


  • Organizational Affiliation
    • Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan. ktani@doc.medic.mie-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 702.95 kDa 
  • Atom Count: 46,292 
  • Modeled Residue Count: 4,534 
  • Deposited Residue Count: 4,820 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitA [auth L],
HA [auth l]
281Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M],
IA [auth m]
307Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center subunit HC [auth H],
JA [auth h]
260Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PufXFA [auth X],
MB [auth x]
81Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
protein-UGA [auth U],
NB [auth u]
53Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 

Small Molecules

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

Query on CDL



Download:Ideal Coordinates CCD File
DG [auth m]
GF [auth X]
GG [auth m]
GJ [auth x]
HF [auth X]
DG [auth m],
GF [auth X],
GG [auth m],
GJ [auth x],
HF [auth X],
IC [auth M],
IF [auth X],
JE [auth Y],
JI [auth y],
LD [auth K],
LG [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
(Subject of Investigation/LOI)

Query on BCL



Download:Ideal Coordinates CCD File
AC [auth M]
AE [auth R]
AF [auth 5]
BD [auth F]
BE [auth S]
AC [auth M],
AE [auth R],
AF [auth 5],
BD [auth F],
BE [auth S],
BJ [auth 06],
CF [auth 6],
CH [auth g],
CJ [auth 07],
DI [auth t],
ED [auth G],
EE [auth T],
EF [auth 7],
EI [auth v],
EJ [auth 08],
FF [auth 8],
FH [auth i],
GE [auth V],
HD [auth I],
HH [auth j],
HI [auth w],
IE [auth W],
IH [auth k],
KD [auth J],
KE [auth Y],
KI [auth y],
MD [auth K],
ME [auth Z],
MF [auth l],
MH [auth n],
NG [auth a],
OB [auth L],
OE [auth 1],
OH [auth o],
OI [auth z],
PG [auth b],
PI [auth 01],
QD [auth N],
QG [auth d],
QH [auth p],
RC [auth A],
RD [auth O],
RE [auth 2],
SI [auth 02],
TG [auth e],
TH [auth q],
UC [auth B],
UD [auth P],
UE [auth 3],
UF [auth m],
VF [auth m],
VG [auth f],
VI [auth 03],
WC [auth D],
WF [auth m],
WH [auth r],
XD [auth Q],
XE [auth 4],
XI [auth 04],
YB [auth L],
YC [auth E],
YI [auth 05],
ZB [auth M],
ZH [auth s]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
BC [auth M],
NF [auth l],
PB [auth L],
XF [auth m]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



Download:Ideal Coordinates CCD File
DC [auth M]
OF [auth l]
PF [auth l]
QB [auth L]
RB [auth L]
DC [auth M],
OF [auth l],
PF [auth l],
QB [auth L],
RB [auth L],
RG [auth d],
XC [auth D],
ZF [auth m]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
CD [auth F]
EG [auth m]
FG [auth m]
FJ [auth x]
HG [auth h]
CD [auth F],
EG [auth m],
FG [auth m],
FJ [auth x],
HG [auth h],
JC [auth M],
KH [auth k],
LC [auth H],
LI [auth y],
MG [auth h],
ND [auth K],
NE [auth 1],
OC [auth H],
PC [auth H],
QF [auth l],
RF [auth l],
SF [auth l],
SH [auth q],
TF [auth l],
UB [auth L],
VB [auth L],
WB [auth L],
WD [auth Q],
WG [auth f],
XB [auth L],
XG [auth f]
(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
PTY

Query on PTY



Download:Ideal Coordinates CCD File
AD [auth F],
KG [auth h],
NC [auth H],
YG [auth f]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
SPO

Query on SPO



Download:Ideal Coordinates CCD File
AG [auth m]
AH [auth g]
AI [auth s]
AJ [auth 05]
BF [auth 5]
AG [auth m],
AH [auth g],
AI [auth s],
AJ [auth 05],
BF [auth 5],
BH [auth g],
CE [auth S],
CI [auth s],
DD [auth G],
DE [auth S],
DF [auth 6],
DJ [auth 08],
EC [auth M],
FD [auth G],
FE [auth T],
FI [auth v],
GH [auth j],
GI [auth w],
HE [auth V],
ID [auth I],
JD [auth J],
JH [auth k],
LE [auth Y],
LH [auth n],
MI [auth y],
NH [auth n],
NI [auth z],
OD [auth K],
OG [auth a],
PD [auth N],
PE [auth 2],
PH [auth p],
QE [auth 2],
QI [auth 01],
RI [auth 01],
SC [auth A],
SD [auth O],
SE [auth 2],
SG [auth e],
TC [auth B],
TD [auth P],
TI [auth 02],
UG [auth f],
UH [auth q],
VC [auth B],
VE [auth 3],
VH [auth r],
XH [auth r],
YD [auth Q],
YE [auth 4],
ZC [auth E],
ZD [auth R],
ZG [auth f],
ZI [auth 05]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BG [auth m]
BI [auth s]
CG [auth m]
DH [auth i]
EH [auth i]
BG [auth m],
BI [auth s],
CG [auth m],
DH [auth i],
EH [auth i],
FC [auth M],
GC [auth M],
GD [auth I],
HC [auth M],
IG [auth h],
JF [auth U],
JG [auth h],
KC [auth M],
KF [auth U],
LF [auth U],
MC [auth H],
QC [auth A],
RH [auth q],
SB [auth L],
TB [auth L],
TE [auth 3],
UI [auth 03],
VD [auth Q],
WE [auth 3],
WI [auth 03],
YH [auth s],
ZE [auth 5]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
II [auth y]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
CC [auth M],
YF [auth m]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
AB [auth v]
BA [auth 5]
CB [auth y]
D [auth A]
DA [auth 7]
AB [auth v],
BA [auth 5],
CB [auth y],
D [auth A],
DA [auth 7],
EB [auth 01],
F [auth D],
GB [auth 03],
H [auth F],
IB [auth 05],
J [auth I],
KA [auth a],
KB [auth 07],
L [auth K],
MA [auth d],
N [auth O],
OA [auth f],
P [auth Q],
QA [auth i],
R [auth S],
SA [auth k],
T [auth V],
UA [auth o],
V [auth Y],
WA [auth q],
X [auth 1],
YA [auth s],
Z [auth 3]
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report

Currently 7VY2 does not have a validation slider image.



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: 2022-04-27
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary