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- PDB-9klm: Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH... -

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Basic information

Entry
Database: PDB / ID: 9klm
TitleCryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex
Components
  • (Reaction center protein ...) x 3
  • Antenna pigment protein beta chain
  • Intrinsic membrane protein PufX
  • Light-harvesting protein B-875 alpha chain
  • protein-U
KeywordsPHOTOSYNTHESIS / LH1-RC / Rhodobacter sphaeroides G1C / neurosporene
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / PRC-barrel domain / PRC-barrel-like superfamily / Photosynthetic reaction centre, L subunit / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / Chem-PGV / UBIQUINONE-10 / : / Light-harvesting protein B-875 alpha chain / Reaction center protein H chain ...: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / Chem-PGV / UBIQUINONE-10 / : / Light-harvesting protein B-875 alpha chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Intrinsic membrane protein PufX / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWu, Y.-L. / Yu, L.-J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: Photosynth Res / Year: 2025
Title: Molecular and structural insights into neurosporene accumulation in Rhodobacter sphaeroides G1C.
Authors: Yu-Lu Wu / Guang-Lei Wang / Xiang-Ping Wang / Xing-Yu Yue / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Richard J Cogdell / Long-Jiang Yu /
Abstract: Carotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid ...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.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
A: Light-harvesting protein B-875 alpha chain
a: Antenna pigment protein beta chain
B: Light-harvesting protein B-875 alpha chain
b: Antenna pigment protein beta chain
C: Light-harvesting protein B-875 alpha chain
c: Antenna pigment protein beta chain
D: Light-harvesting protein B-875 alpha chain
d: Antenna pigment protein beta chain
E: Light-harvesting protein B-875 alpha chain
e: Antenna pigment protein beta chain
F: Light-harvesting protein B-875 alpha chain
f: Antenna pigment protein beta chain
G: Light-harvesting protein B-875 alpha chain
g: Antenna pigment protein beta chain
I: Light-harvesting protein B-875 alpha chain
i: Antenna pigment protein beta chain
J: Light-harvesting protein B-875 alpha chain
j: Antenna pigment protein beta chain
K: Light-harvesting protein B-875 alpha chain
k: Antenna pigment protein beta chain
N: Light-harvesting protein B-875 alpha chain
n: Antenna pigment protein beta chain
O: Light-harvesting protein B-875 alpha chain
o: Antenna pigment protein beta chain
P: Light-harvesting protein B-875 alpha chain
p: Antenna pigment protein beta chain
Q: Light-harvesting protein B-875 alpha chain
q: Antenna pigment protein beta chain
U: protein-U
X: Intrinsic membrane protein PufX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,887150
Polymers278,09233
Non-polymers78,795117
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Reaction center protein ... , 3 types, 3 molecules LMH

#1: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31476.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y8
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34557.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y9
#3: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y7

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Protein , 3 types, 16 molecules ABCDEFGIJKNOPQUX

#4: Protein
Light-harvesting protein B-875 alpha chain / light-harvesting protein alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6473.780 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0X9
#6: Protein protein-U


Mass: 5583.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: A0AAN4RAQ9
#7: Protein Intrinsic membrane protein PufX / PUFX protien


Mass: 9089.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q7B2Z6

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Protein/peptide / Sugars , 2 types, 39 molecules abcdefgijknopq

#13: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#5: Protein/peptide
Antenna pigment protein beta chain / light-harvesting protein beta chain


Mass: 5620.372 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q7B300

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Non-polymers , 8 types, 92 molecules

#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#12: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#14: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical...
ChemComp-A1EF2 / (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 / Neurosporene / Neurosporin


Mass: 538.889 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H58 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LH1-RC core complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50.61 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118603 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00624377
ELECTRON MICROSCOPYf_angle_d1.23733259
ELECTRON MICROSCOPYf_dihedral_angle_d18.3749810
ELECTRON MICROSCOPYf_chiral_restr0.1823362
ELECTRON MICROSCOPYf_plane_restr0.0053707

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