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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 / membrane / 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, M subunit / 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 / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / 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: To Be Published
Title: From Genome to structure: Elucidating Neurosporene Production in the Rhodobacter sphaeroides G1C Mutant
Authors: Wu, Y.-L. / Yu, L.-J.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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