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- EMDB-63365: Cryo-EM structure of light harvesting complex 2 from Ery. sanguineus -

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Basic information

Entry
Database: EMDB / ID: EMD-63365
TitleCryo-EM structure of light harvesting complex 2 from Ery. sanguineus
Map data
Sample
  • Complex: light harvesting complex 2
    • Protein or peptide: Light-harvesting protein B-800/814 alpha chain
    • Protein or peptide: Light-harvesting protein B-800-850 beta chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: (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
Keywordslight harvesting complex 2 / Erythrobacte sanguineus / photosynthesis
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
Light-harvesting protein B-800-850 beta chain
Similarity search - Component
Biological speciesErythrobacter sanguineus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsYue X-Y / Wang G-L / Yu L-J
Funding support China, 3 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63365.png

Downloads & links

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Map

FileDownload / File: emd_63365.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5105488 - 0.91195273
Average (Standard dev.)0.0035079033 (±0.027646976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63365_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_63365_half_map_2.map
Projections & Slices
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Sample components

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Entire : light harvesting complex 2

EntireName: light harvesting complex 2
Components
  • Complex: light harvesting complex 2
    • Protein or peptide: Light-harvesting protein B-800/814 alpha chain
    • Protein or peptide: Light-harvesting protein B-800-850 beta chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: (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

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Supramolecule #1: light harvesting complex 2

SupramoleculeName: light harvesting complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Erythrobacter sanguineus (bacteria)

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

MacromoleculeName: Light-harvesting protein B-800/814 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 7.290368 KDa
SequenceString:
MNEGRIFLYV SPEVILPIMF LILVLTSLTV HFAILINTTW FGDFFQGSAG EFAAAPAAAD ANAAPWE

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Macromolecule #2: Light-harvesting protein B-800-850 beta chain

MacromoleculeName: Light-harvesting protein B-800-850 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 5.596477 KDa
SequenceString:
MAGDDTKVYP TGLTEAQALE INDGLKWGTR IYFGIAVAAH ILAFILTPWL K

UniProtKB: Light-harvesting protein B-800-850 beta chain

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 27 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-2-[(1~{Z},3...

MacromoleculeName: (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] ...Name: (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
type: ligand / ID: 4 / Number of copies: 9 / Formula: A1ELD
Molecular weightTheoretical: 596.882 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7eqd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119391
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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