8B64

Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus.

Bracun, L.Yamagata, A.Christianson, B.M.Shirouzu, M.Liu, L.N.

(2023) Structure 31: 318

  • DOI: https://doi.org/10.1016/j.str.2023.01.006
  • Primary Citation of Related Structures:  
    8B64

  • PubMed Abstract: 

    In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial photosynthesis. Here, we report a 2.59-Å resolution cryoelectron microscopy (cryo-EM) structure of the RC-LH1 supercomplex from Rhodobacter capsulatus. We show that Rba. capsulatus RC-LH1 complexes are exclusively monomers in which the RC is surrounded by a 15-subunit LH1 ring. Incorporation of a transmembrane polypeptide PufX leads to a large opening within the LH1 ring. Each LH1 subunit associates two carotenoids and two bacteriochlorophylls, which is similar to Rba. sphaeroides RC-LH1 but more than one carotenoid per LH1 in Rba. veldkampii RC-LH1 monomer. Collectively, the unique Rba. capsulatus RC-LH1-PufX represents an intermediate structure between Rba. sphaeroides and Rba. veldkampii RC-LH1-PufX. Comparison of PufX from the three Rhodobacter species indicates the important residues involved in dimerization of RC-LH1.


  • Organizational Affiliation

    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-870 alpha chain58Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02948 (Rhodobacter capsulatus)
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UniProt GroupP02948
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 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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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXG [auth X]78Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26240 (Rhodobacter capsulatus)
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UniProt GroupP26240
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainH [auth L]282Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19057 (Rhodobacter capsulatus)
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UniProt GroupP19057
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainI [auth M]307Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P11847 (Rhodobacter capsulatus)
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UniProt GroupP11847
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainJ [auth H]254Rhodobacter capsulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19056 (Rhodobacter capsulatus)
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth r]
BB [auth M]
BD [auth F]
CC [auth r]
DC [auth O]
AC [auth r],
BB [auth M],
BD [auth F],
CC [auth r],
DC [auth O],
DD [auth f],
FB [auth M],
GC [auth o],
HB [auth M],
IA [auth a],
IC [auth n],
JA [auth e],
JC [auth n],
KA [auth e],
LA [auth D],
LC [auth K],
MB [auth d],
NA [auth b],
OA [auth b],
OC [auth k],
QC [auth j],
RA [auth A],
RB [auth t],
SC [auth I],
VA [auth L],
VB [auth T],
VC [auth J],
WB [auth s],
WC [auth i],
XB [auth s],
YB [auth U],
YC [auth g],
ZB [auth U],
ZC [auth g]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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IB [auth M],
WA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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DB [auth M],
XA [auth L],
YA [auth L],
ZA [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
3PE
Query on 3PE

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AB [auth L]
GB [auth M]
JB [auth M]
KB [auth H]
LB [auth H]
AB [auth L],
GB [auth M],
JB [auth M],
KB [auth H],
LB [auth H],
OB [auth d],
PB [auth d]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
SPO (Subject of Investigation/LOI)
Query on SPO

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AD [auth F]
BC [auth r]
CD [auth G]
EB [auth M]
EC [auth O]
AD [auth F],
BC [auth r],
CD [auth G],
EB [auth M],
EC [auth O],
ED [auth f],
FC [auth R],
HC [auth o],
KC [auth K],
MA [auth D],
MC [auth K],
NB [auth d],
NC [auth N],
PA [auth b],
PC [auth k],
QA [auth A],
QB [auth B],
RC [auth j],
SA [auth E],
SB [auth t],
TA [auth E],
TB [auth S],
TC [auth I],
UA [auth E],
UB [auth S],
UC [auth J],
XC [auth i]
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
CB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2024-07-24
    Changes: Data collection