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- EMDB-63370: Cryo-EM structure of LH1-RC from Ery. sanguineus -

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Basic information

Entry
Database: EMDB / ID: EMD-63370
TitleCryo-EM structure of LH1-RC from Ery. sanguineus
Map data
Sample
  • Complex: LH1-RC
    • Protein or peptide: x 6 types
  • Ligand: x 13 types
Keywordslight harvesting complex 2 / Erythrobacte sanguineus / photosynthesis
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 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 6, 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_63370.png

Downloads & links

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Map

FileDownload / File: emd_63370.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0961
Minimum - Maximum-0.53226733 - 0.8944612
Average (Standard dev.)0.0023010585 (±0.019132657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 323.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63370_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63370_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : LH1-RC

EntireName: LH1-RC
Components
  • Complex: LH1-RC
    • Protein or peptide: Light-harvesting complex 1 alpha chain
    • Protein or peptide: Antenna complex alpha/beta subunit
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Photosynthetic reaction center H subunit
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Secreted protein
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: (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
  • 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
  • Ligand: Octadecane
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: Ubiquinone-8
  • Ligand: FE (III) ION
  • Ligand: (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
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: PHOSPHATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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Supramolecule #1: LH1-RC

SupramoleculeName: LH1-RC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Erythrobacter sanguineus (bacteria)

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Macromolecule #1: Light-harvesting complex 1 alpha chain

MacromoleculeName: Light-harvesting complex 1 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 7.175297 KDa
SequenceString:
MWRIWFYFDI RRALVALHVG LAVLAFTIHF ILLSTDRYNW LERAPGAPAP VQAAIESSEA PAAG

UniProtKB: Light-harvesting complex 1 alpha chain

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Macromolecule #2: Antenna complex alpha/beta subunit

MacromoleculeName: Antenna complex alpha/beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 5.817729 KDa
SequenceString:
MADPTPGERV GTYLTPEEAQ EIHKGFMGTF VLYVAIALVA HALMWAYKPW FG

UniProtKB: Antenna complex alpha/beta subunit

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Macromolecule #3: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 30.142752 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA ISALLGTALI FAAAAQGPTL NPWLISINPP SIEAGLAFAP LSEGGYWQV ITACAVVAFS SWVLRQAEIS RKLGMSYHVP IAFGVAVFAY VTLNVIRPLW MGAWGNGFPY GIWTHLDWVS N VGYAFGNF ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA ISALLGTALI FAAAAQGPTL NPWLISINPP SIEAGLAFAP LSEGGYWQV ITACAVVAFS SWVLRQAEIS RKLGMSYHVP IAFGVAVFAY VTLNVIRPLW MGAWGNGFPY GIWTHLDWVS N VGYAFGNF HYNPVHMLAI TFFFTNCLAL ALHGGLVLSA VNPTGGTDVK TPEYEDTYFR DFIGYSVGTL GIHRVGLFLA LN AGFWSAI CIVISGTLYV GSWIEFWDFW KKIPIWS

UniProtKB: Reaction center protein L chain

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Macromolecule #4: Photosynthetic reaction center H subunit

MacromoleculeName: Photosynthetic reaction center H subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 29.917133 KDa
SequenceString: MNHAYIVGTF DVAELAFLLF FGFFIALVFY LNRESRREGY PLEDEQTGKI HPGSLFDGDK KAFQLPHGRG TYVPENVARD DINVPGVRS FRSAGAPWVP TGDPMKDGMG PAAWANRSKY PDLTFDGRPR IVPIAQSHEL IIAPNDPQLI GWPVMAADKK M VGKVSDIW ...String:
MNHAYIVGTF DVAELAFLLF FGFFIALVFY LNRESRREGY PLEDEQTGKI HPGSLFDGDK KAFQLPHGRG TYVPENVARD DINVPGVRS FRSAGAPWVP TGDPMKDGMG PAAWANRSKY PDLTFDGRPR IVPIAQSHEL IIAPNDPQLI GWPVMAADKK M VGKVSDIW VDQAEHMIRY LEVETTTGKK VLAPMMVASV HGNSLIDALL PIVEDKPKFV EIDAITAAQF EDVPALETPG II TRYEEDR VQAYFGGGYM YAMPERAEPW L

UniProtKB: Photosynthetic reaction center H subunit

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Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 36.107172 KDa
SequenceString: MATYQNIFTQ VQVTGPPEMG VPHLDGSEGR VELTGHNYWL GKIGQAQIGP IYLGLLGTIS LTFGAAAIMI IGLNFWAQAG WSPQTFMRE FFWLSLDPPG PEYGFSPFVP LNEGGWFIMA GAFLTIAVLT WWARTYTRAK ALGMGMHIPW AFASAIWLFL V LGFIRPML ...String:
MATYQNIFTQ VQVTGPPEMG VPHLDGSEGR VELTGHNYWL GKIGQAQIGP IYLGLLGTIS LTFGAAAIMI IGLNFWAQAG WSPQTFMRE FFWLSLDPPG PEYGFSPFVP LNEGGWFIMA GAFLTIAVLT WWARTYTRAK ALGMGMHIPW AFASAIWLFL V LGFIRPML LGDWSEAVPY GIFSHLDWTN NFSLRYGNLF YNPFHALSIV FLYGSAVLFA MHGATILALG RYGGEREIEQ IT DRGTAAE RGALFWRWVM GFNATFESIH RWAWWFAVLT TLTGGIGILI TGTVVDNWYL WAQEHYYAPE TFNYDPSGAI AGS TGQ

UniProtKB: Reaction center protein M chain

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Macromolecule #6: Secreted protein

MacromoleculeName: Secreted protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Erythrobacter sanguineus (bacteria)
Molecular weightTheoretical: 13.297557 KDa
SequenceString:
MKLHVILTGA AALALTACSG NTASGNIAAE QAAQEAASAP AVEETPVAST FPESVGAFGD GYPEAGDPCR NLGETAATSN YLDDSAILA GCPDTASAEA LGGEIVDTVD GIIMVMVPQG DTMAPPTTLE GAAPEE

UniProtKB: Secreted protein

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 36 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #8: (1~{R},2~{R})-3,3,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},1...

MacromoleculeName: (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- ...Name: (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
type: ligand / ID: 8 / Number of copies: 16 / Formula: A1EL2
Molecular weightTheoretical: 584.871 Da

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Macromolecule #9: (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: 9 / Number of copies: 16 / Formula: A1ELD
Molecular weightTheoretical: 596.882 Da

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Macromolecule #10: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 10 / Number of copies: 11 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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Macromolecule #11: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 11 / Number of copies: 8 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #13: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 13 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #14: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 14 / Number of copies: 3 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #15: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #16: (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~...

MacromoleculeName: (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
type: ligand / ID: 16 / Number of copies: 1 / Formula: H4X
Molecular weightTheoretical: 600.956 Da
Chemical component information

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

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Macromolecule #17: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 17 / Number of copies: 1 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #18: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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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: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210570
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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