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- PDB-9lti: Cryo-EM structure of LH1-RC from Ery. sanguineus -

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Basic information

Entry
Database: PDB / ID: 9lti
TitleCryo-EM structure of LH1-RC from Ery. sanguineus
Components
  • (Reaction center protein ...) x 2
  • Antenna complex alpha/beta subunit
  • Light-harvesting complex 1 alpha chain
  • Photosynthetic reaction center H subunit
  • Secreted protein
KeywordsPHOTOSYNTHESIS / light harvesting complex 2 / Erythrobacte sanguineus
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 / endomembrane system / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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 / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Octadecane / : / : / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / Chem-H4X / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV ...Octadecane / : / : / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / Chem-H4X / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / PHOSPHATE ION / Ubiquinone-8 / Light-harvesting complex 1 alpha chain / Antenna complex alpha/beta subunit / Reaction center protein L chain / Photosynthetic reaction center H subunit / Reaction center protein M chain / Secreted protein
Similarity search - Component
Biological speciesErythrobacter sanguineus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsYue, X.-Y. / Wang, G.-L. / Yu, L.-J.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)ZR2019ZD48 China
Ministry of Science and Technology (MoST, China)2022SZX12 China
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structures of photocomplexes from the free-living aerobic anoxygenic phototrophic bacterium Erythrobacter sanguineus.
Authors: Xing-Yu Yue / Guang-Lei Wang / Mei-Juan Zou / Fei Ma / Zheng-Yu Wang-Otomo / Michael T Madigan / Long-Jiang Yu /
Abstract: Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional ...Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph Erythrobacter (Ery.) sanguineus. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin-pigments that are absent from anaerobic anoxygenic phototrophs-to form a closed ring structure. Ery. sanguineus LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The Ery. sanguineus LH2 complex shows unique absorption characteristics, with its Q transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light-harvesting complex 1 alpha chain
B: Light-harvesting complex 1 alpha chain
C: Light-harvesting complex 1 alpha chain
D: Light-harvesting complex 1 alpha chain
E: Light-harvesting complex 1 alpha chain
F: Light-harvesting complex 1 alpha chain
G: Light-harvesting complex 1 alpha chain
Q: Light-harvesting complex 1 alpha chain
I: Light-harvesting complex 1 alpha chain
J: Light-harvesting complex 1 alpha chain
K: Light-harvesting complex 1 alpha chain
R: Light-harvesting complex 1 alpha chain
S: Light-harvesting complex 1 alpha chain
N: Light-harvesting complex 1 alpha chain
O: Light-harvesting complex 1 alpha chain
P: Light-harvesting complex 1 alpha chain
b: Antenna complex alpha/beta subunit
a: Antenna complex alpha/beta subunit
p: Antenna complex alpha/beta subunit
o: Antenna complex alpha/beta subunit
n: Antenna complex alpha/beta subunit
s: Antenna complex alpha/beta subunit
r: Antenna complex alpha/beta subunit
k: Antenna complex alpha/beta subunit
j: Antenna complex alpha/beta subunit
c: Antenna complex alpha/beta subunit
d: Antenna complex alpha/beta subunit
e: Antenna complex alpha/beta subunit
f: Antenna complex alpha/beta subunit
g: Antenna complex alpha/beta subunit
q: Antenna complex alpha/beta subunit
i: Antenna complex alpha/beta subunit
L: Reaction center protein L chain
H: Photosynthetic reaction center H subunit
M: Reaction center protein M chain
T: Secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,525136
Polymers317,35336
Non-polymers68,172100
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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Protein , 4 types, 34 molecules ABCDEFGQIJKRSNOPbaponsrkjcdefg...

#1: Protein
Light-harvesting complex 1 alpha chain / LH1 alpha polypeptide


Mass: 7175.297 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7RZ65
#2: Protein
Antenna complex alpha/beta subunit / LH1 beta polypeptide


Mass: 5817.729 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7RZ98
#4: Protein Photosynthetic reaction center H subunit


Mass: 29917.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7RZD6
#6: Protein Secreted protein / Protein 135


Mass: 13297.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7SD26

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Reaction center protein ... , 2 types, 2 molecules LM

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


Mass: 30142.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7RZC0
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 36107.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7RZG6

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Sugars , 1 types, 3 molecules

#12: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 12 types, 97 molecules

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


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-A1EL2 / (1~{R},2~{R})-3,3,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-4-ene-1,2-diol / Caloxanthin


Mass: 584.871 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-A1ELD / (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-2-[(1~{Z},3~{Z},5~{E})-8-methoxy-4,8-dimethyl-nona-1,3,5-trienyl]-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]heptadeca-2,4,6,8,10,12,14,16-octaenal


Mass: 596.882 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C41H56O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H38
#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.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#13: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#15: 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
#16: Chemical ChemComp-H4X / (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene


Mass: 600.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H64O2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#18: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#19: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationN

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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 / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Erythrobacter sanguineus (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: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50.5 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: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210570 / Symmetry type: POINT
RefinementHighest resolution: 2.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01323776
ELECTRON MICROSCOPYf_angle_d1.80732795
ELECTRON MICROSCOPYf_dihedral_angle_d21.389279
ELECTRON MICROSCOPYf_chiral_restr0.2083221
ELECTRON MICROSCOPYf_plane_restr0.0043718

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