9KLM | pdb_00009klm

Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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Literature

Molecular and structural insights into neurosporene accumulation in Rhodobacter sphaeroides G1C.

Wu, Y.L.Wang, G.L.Wang, X.P.Yue, X.Y.Zou, M.J.Wang-Otomo, Z.Y.Madigan, M.T.Cogdell, R.J.Yu, L.J.

(2025) Photosynth Res 163: 53-53

  • DOI: https://doi.org/10.1007/s11120-025-01174-1
  • Primary Citation Related Structures: 
    9KLM

  • PubMed Abstract: 

    Carotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid neurosporene, a key intermediate in carotenoid biosynthesis, plays a central role in the production of several other carotenoids; however, neurosporene accumulation is rare in nature. In this study, we investigated the accumulation of neurosporene in Rhodobacter sphaeroides strain G1C, a mutant derivative of wild-type Rba. sphaeroides 2.4.1 obtained by nitrosoguanidine mutagenesis. Whole-genome sequencing of strain G1C identified a nonsense mutation in the crtC gene resulting in enzyme inactivation and disruption of normal carotenoid biosynthesis. Physiological analysis and cryo-EM structural analysis of the major photosynthetic complexes of strain G1C showed that the accumulation of neurosporene did not significantly alter either the structure or functioning of the light-harvesting complexes and had no perceptible effect on photosynthetic growth. While the carotenoid composition of strain G1C shifts from spheroidene to neurosporene, its photocomplexes remain structurally intact and their physiological properties remain largely unchanged. This study provides genomic insights into the importance of CrtC activity to the production of carotenoids in Rba. sphaeroides and highlights the unexpected finding that carotenoid substitution in photocomplexes can occur without significantly disrupting photocomplex function.


  • Organizational Affiliation
    • Photosynthesis Research Center, State Key Laboratory of Forage Breeding-by-Design and Utilization, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.

Macromolecule Content 

  • Total Structure Weight: 356.89 kDa 
  • Atom Count: 23,521 
  • Modeled Residue Count: 2,280 
  • Deposited Residue Count: 2,427 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]282Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
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]308Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein B-875 alpha chain54Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for P0C0X9 (Cereibacter sphaeroides)
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Entity Groups
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UniProt GroupP0C0X9
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna pigment protein beta chain49Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q7B300 (Cereibacter sphaeroides)
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UniProt GroupQ7B300
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
protein-UFA [auth U]53Cereibacter sphaeroidesMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Intrinsic membrane protein PufXGA [auth X]82Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q7B2Z6 (Cereibacter sphaeroides)
Explore Q7B2Z6 
Go to UniProtKB:  Q7B2Z6
Entity Groups
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UniProt GroupQ7B2Z6
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
(Subject of Investigation/LOI)

Query on CDL



Download:Ideal Coordinates CCD File
FB [auth M],
IB [auth M],
NC [auth E],
VC [auth F]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
(Subject of Investigation/LOI)

Query on BCL



Download:Ideal Coordinates CCD File
AC [auth C]
DC [auth c]
DD [auth G]
DE [auth n]
FD [auth g]
AC [auth C],
DC [auth c],
DD [auth G],
DE [auth n],
FD [auth g],
FE [auth O],
HA [auth L],
HC [auth D],
ID [auth I],
IE [auth o],
KE [auth P],
MC [auth d],
MD [auth i],
ME [auth p],
NE [auth Q],
OA [auth L],
OB [auth A],
OD [auth J],
PC [auth E],
PE [auth q],
QB [auth a],
SB [auth B],
TC [auth e],
TD [auth j],
VD [auth K],
WA [auth M],
WC [auth F],
XB [auth b],
YD [auth k],
ZA [auth M],
ZC [auth f],
ZD [auth N]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
(Subject of Investigation/LOI)

Query on BPH



Download:Ideal Coordinates CCD File
AB [auth M],
IA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
(Subject of Investigation/LOI)

Query on U10



Download:Ideal Coordinates CCD File
CB [auth M],
JA [auth L],
KA [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PGV
(Subject of Investigation/LOI)

Query on PGV



Download:Ideal Coordinates CCD File
CD [auth G]
HB [auth M]
LA [auth L]
LB [auth H]
MA [auth L]
CD [auth G],
HB [auth M],
LA [auth L],
LB [auth H],
MA [auth L],
MB [auth H],
QC [auth E],
TA [auth L],
UA [auth L],
WD [auth K],
XA [auth M],
YB [auth C],
ZB [auth C]
(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
A1EF2
(Subject of Investigation/LOI)

Query on A1EF2



Download:Ideal Coordinates CCD File
AE [auth N]
BC [auth C]
BE [auth N]
CE [auth n]
ED [auth g]
AE [auth N],
BC [auth C],
BE [auth N],
CE [auth n],
ED [auth g],
FC [auth c],
GB [auth M],
GD [auth g],
GE [auth O],
HE [auth o],
JC [auth D],
KC [auth D],
LC [auth d],
LD [auth I],
LE [auth p],
ND [auth J],
OE [auth q],
PD [auth J],
QD [auth J],
RB [auth a],
RC [auth E],
SC [auth e],
SD [auth J],
UB [auth B],
WB [auth b],
XD [auth k],
YC [auth f]
(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,8,10,12,14,16,18,20,22,26,30-dodecaene
C40 H58
ATCICVFRSJQYDV-XILUKMICSA-N
LMT
(Subject of Investigation/LOI)

Query on LMT



Download:Ideal Coordinates CCD File
AD [auth G]
BD [auth G]
CC [auth c]
DB [auth M]
EB [auth M]
AD [auth G],
BD [auth G],
CC [auth c],
DB [auth M],
EB [auth M],
EC [auth c],
EE [auth O],
GC [auth D],
HD [auth I],
IC [auth D],
JB [auth H],
JD [auth I],
JE [auth P],
KB [auth H],
NB [auth A],
OC [auth E],
PB [auth a],
QE [auth U],
RA [auth L],
SA [auth L],
TB [auth B],
TE [auth X],
UC [auth F],
VA [auth L],
VB [auth b]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA
(Subject of Investigation/LOI)

Query on LDA



Download:Ideal Coordinates CCD File
KD [auth I]
NA [auth L]
PA [auth L]
QA [auth L]
RD [auth J]
KD [auth I],
NA [auth L],
PA [auth L],
QA [auth L],
RD [auth J],
RE [auth X],
SE [auth X],
UD [auth K],
XC [auth F],
YA [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
BB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth L]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
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-07-08
    Changes: Data collection, Database references