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- PDB-9lt4: Cryo-EM structure of light harvesting complex 2 from Ery. sanguineus -

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Basic information

Entry
Database: PDB / ID: 9lt4
TitleCryo-EM structure of light harvesting complex 2 from Ery. sanguineus
Components
  • Light-harvesting protein B-800-850 beta chain
  • Light-harvesting protein B-800/814 alpha chain
KeywordsPHOTOSYNTHESIS / light harvesting complex 2 / Erythrobacte sanguineus
Function / homology
Function and homology information


plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
: / BACTERIOCHLOROPHYLL A / Light-harvesting protein B-800-850 beta chain
Similarity search - Component
Biological speciesErythrobacter sanguineus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 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 5, 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 protein B-800/814 alpha chain
i: Light-harvesting protein B-800-850 beta chain
a: Light-harvesting protein B-800-850 beta chain
I: Light-harvesting protein B-800/814 alpha chain
H: Light-harvesting protein B-800/814 alpha chain
G: Light-harvesting protein B-800/814 alpha chain
F: Light-harvesting protein B-800/814 alpha chain
E: Light-harvesting protein B-800/814 alpha chain
D: Light-harvesting protein B-800/814 alpha chain
C: Light-harvesting protein B-800/814 alpha chain
B: Light-harvesting protein B-800/814 alpha chain
h: Light-harvesting protein B-800-850 beta chain
g: Light-harvesting protein B-800-850 beta chain
f: Light-harvesting protein B-800-850 beta chain
e: Light-harvesting protein B-800-850 beta chain
d: Light-harvesting protein B-800-850 beta chain
c: Light-harvesting protein B-800-850 beta chain
b: Light-harvesting protein B-800-850 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,96454
Polymers115,98218
Non-polymers29,98336
Water00
1


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

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Components

#1: Protein
Light-harvesting protein B-800/814 alpha chain


Mass: 7290.368 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria)
#2: Protein
Light-harvesting protein B-800-850 beta chain


Mass: 5596.477 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Erythrobacter sanguineus (bacteria) / References: UniProt: A0A1M7SGD0
#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 9 / Source method: obtained synthetically / Formula: C41H56O3 / Feature type: SUBJECT OF INVESTIGATION
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: light harvesting complex 2 / Type: COMPLEX / Entity ID: #1-#2 / 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119391 / Symmetry type: POINT
RefinementHighest resolution: 2.74 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049414
ELECTRON MICROSCOPYf_angle_d1.1113203
ELECTRON MICROSCOPYf_dihedral_angle_d20.1292250
ELECTRON MICROSCOPYf_chiral_restr0.0431386
ELECTRON MICROSCOPYf_plane_restr0.0051422

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