7VY2

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 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitA [auth L],
HA [auth l]
281Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M],
IA [auth m]
307Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center subunit HC [auth H],
JA [auth h]
260Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein alpha chain54Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain48Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PufXFA [auth X],
MB [auth x]
81Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
protein-UGA [auth U],
NB [auth u]
53Cereibacter sphaeroides f. sp. denitrificansMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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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

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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

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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

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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

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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

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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

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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

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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

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II [auth y]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE
Query on FE

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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

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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