7YML

Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex.

Tani, K.Kanno, R.Ji, X.C.Satoh, I.Kobayashi, Y.Hall, M.Yu, L.J.Kimura, Y.Mizoguchi, A.Humbel, B.M.Madigan, M.T.Wang-Otomo, Z.Y.

(2023) Nat Commun 14: 846-846

  • DOI: https://doi.org/10.1038/s41467-023-36460-w
  • Primary Citation of Related Structures:  
    7YML

  • PubMed Abstract: 

    Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the light-harvesting 1-reaction center (LH1-RC) complex, but lacks protein-U, a U-shaped polypeptide in the LH1-RC of its close relative Rba. sphaeroides. Here we present a cryo-EM structure of the Rba. capsulatus LH1-RC purified by DEAE chromatography. The crescent-shaped LH1-RC exhibits a compact structure containing only 10 LH1 αβ-subunits. Four αβ-subunits corresponding to those adjacent to protein-U in Rba. sphaeroides were absent. PufX in Rba. capsulatus exhibits a unique conformation in its N-terminus that self-associates with amino acids in its own transmembrane domain and interacts with nearby polypeptides, preventing it from interacting with proteins in other complexes and forming dimeric structures. These features are discussed in relation to the minimal requirements for the formation of LH1-RC monomers and dimers, the spectroscopic behavior of both the LH1 and RC, and the bioenergetics of energy transfer from LH1 to the RC.


  • Organizational Affiliation

    Graduate School of Medicine, Mie University, Tsu, Japan. ktani@doc.medic.mie-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]282Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19057 (Rhodobacter capsulatus)
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Go to UniProtKB:  P19057
Entity Groups  
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UniProt GroupP19057
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P11847 (Rhodobacter capsulatus)
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Go to UniProtKB:  P11847
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UniProt GroupP11847
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitC [auth H]253Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19056 (Rhodobacter capsulatus)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19056
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-870 alpha chain58Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02948 (Rhodobacter capsulatus)
Explore P02948 
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UniProt GroupP02948
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-870 beta chain49Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02950 (Rhodobacter capsulatus)
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UniProt GroupP02950
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center PufX protein78Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26240 (Rhodobacter capsulatus)
Explore P26240 
Go to UniProtKB:  P26240
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UniProt GroupP26240
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AD [auth V]
BC [auth J]
CD [auth W]
DC [auth K]
ED [auth Y]
AD [auth V],
BC [auth J],
CD [auth W],
DC [auth K],
ED [auth Y],
FC [auth N],
GD [auth Z],
HA [auth L],
HB [auth A],
HC [auth O],
JB [auth B],
LA [auth M],
LB [auth D],
LC [auth P],
MA [auth M],
QB [auth E],
QC [auth Q],
RB [auth F],
SC [auth R],
TB [auth F],
VB [auth G],
VC [auth S],
Y [auth L],
YB [auth I],
ZC [auth T]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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NA [auth M],
Z [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
Query on U10

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AA [auth L],
BA [auth L],
JA [auth M],
PA [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PGV
Query on PGV

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CA [auth L]
FB [auth H]
GB [auth H]
KA [auth M]
OC [auth Q]
CA [auth L],
FB [auth H],
GB [auth H],
KA [auth M],
OC [auth Q],
VA [auth M],
WA [auth M],
XA [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
PEE
Query on PEE

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DA [auth L]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
SPO
Query on SPO

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AC [auth I]
BD [auth W]
EC [auth N]
IC [auth O]
JC [auth O]
AC [auth I],
BD [auth W],
EC [auth N],
IC [auth O],
JC [auth O],
KB [auth D],
KC [auth P],
MB [auth D],
OB [auth D],
PB [auth E],
QA [auth M],
RC [auth R],
UB [auth F],
WB [auth G],
WC [auth S],
XC [auth S],
YC [auth T],
ZB [auth I]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LMT
Query on LMT

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CC [auth K]
DD [auth Y]
FA [auth L]
FD [auth Y]
GA [auth L]
CC [auth K],
DD [auth Y],
FA [auth L],
FD [auth Y],
GA [auth L],
HD [auth X],
IA [auth L],
IB [auth A],
ID [auth X],
MC [auth Q],
RA [auth M],
SA [auth M],
TA [auth M],
TC [auth S],
UA [auth M],
UC [auth S],
XB [auth I],
ZA [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA
Query on LDA

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AB [auth M]
BB [auth M]
CB [auth M]
DB [auth H]
EA [auth L]
AB [auth M],
BB [auth M],
CB [auth M],
DB [auth H],
EA [auth L],
EB [auth H],
GC [auth O],
NB [auth D],
NC [auth Q],
PC [auth Q],
YA [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
MYR
Query on MYR

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SB [auth F]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FE
Query on FE

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OA [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
D [auth A]
F [auth D]
H [auth F]
J [auth I]
L [auth K]
D [auth A],
F [auth D],
H [auth F],
J [auth I],
L [auth K],
N [auth O],
P [auth Q],
R [auth S],
T [auth V],
V [auth Y]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references