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- EMDB-62409: Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH... -

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Basic information

Entry
Database: EMDB / ID: EMD-62409
TitleCryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex
Map data
Sample
  • Complex: LH1-RC core complex
    • Protein or peptide: x 7 types
  • Ligand: x 9 types
KeywordsLH1-RC / Rhodobacter sphaeroides G1C / neurosporene / 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 / 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
: / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWu Y-L / Yu L-J
Funding support China, 1 items
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, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62409.png

Downloads & links

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Map

FileDownload / File: emd_62409.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.8276123 - 1.5199637
Average (Standard dev.)0.00029275846 (±0.036949787)
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_62409_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_62409_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LH1-RC core complex

EntireName: LH1-RC core complex
Components
  • Complex: LH1-RC core complex
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Reaction center protein H chain
    • Protein or peptide: Light-harvesting protein B-875 alpha chain
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: protein-U
    • Protein or peptide: Intrinsic membrane protein PufX
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: CARDIOLIPIN
  • Ligand: (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

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Supramolecule #1: LH1-RC core complex

SupramoleculeName: LH1-RC core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Cereibacter sphaeroides (bacteria)

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Macromolecule #1: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 31.476529 KDa
SequenceString: (FME)ALLSFEQKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGL GGA PLAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLD WV SNTGYTYGNF ...String:
(FME)ALLSFEQKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGL GGA PLAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLD WV SNTGYTYGNF HYNPAHMIAI SFFFTNALAL ALHGALVLSA ANPEKGKEMR TPDHEDTFFR DLVGYSIGTL GIHRLGLL L SLSAVFFSAL CMIITGTIWF DQWVDWWQWW VKLPWWANIP GGING

UniProtKB: Reaction center protein L chain

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Macromolecule #2: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 34.557746 KDa
SequenceString: (FME)AEYQNIFSQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFW YQA GWNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIW LW MVLGFIRPIL ...String:
(FME)AEYQNIFSQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFW YQA GWNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIW LW MVLGFIRPIL MGSWSEAVPY GIFSHLDWTN NFSLVHGNLF YNPFHGLSIA FLYGSALLFA MHGATILAVS RFGGEREL E QIADRGTAAE RAALFWRWTM GFNATMEGIH RWAIWMAVLV TLTGGIGILL SGTVVDNWYV WGQNHGMAPL N

UniProtKB: Reaction center protein M chain

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Macromolecule #3: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 28.066322 KDa
SequenceString: MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW ...String:
MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW VDIPEQMARF LEVELKDGST RLLPMQMVKV QSNRVHVNAL SSDLFAGIPT IKSPTEVTLL EEDKICGYVA GG LMYAAPK RKSVVAAMLA EYA

UniProtKB: Reaction center protein H chain

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Macromolecule #4: Light-harvesting protein B-875 alpha chain

MacromoleculeName: Light-harvesting protein B-875 alpha chain / type: protein_or_peptide / ID: 4 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 6.47378 KDa
SequenceString:
(FME)SKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRV

UniProtKB: Light-harvesting protein B-875 alpha chain

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Macromolecule #5: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 5.620372 KDa
SequenceString:
(FME)ADKSDLGYT GLTDEQAQEL HSVYMSGLWL FSAVAIVAHL AVYIWRPWF

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #6: protein-U

MacromoleculeName: protein-U / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 5.583568 KDa
SequenceString:
(FME)PEVSEFAFR LMMAAVIFVG VGIMFAFAGG HWFVGLVVGG LVAAFFAATP NSN

UniProtKB: UNIPROTKB: A0AAN4RAQ9

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Macromolecule #7: Intrinsic membrane protein PufX

MacromoleculeName: Intrinsic membrane protein PufX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 9.089655 KDa
SequenceString:
(FME)ADKTIFNDH LNTNPKTNLR LWVAFQMMKG AGWAGGVFFG TLLLIGFFRV VGRMLPIQEN QAPAPNITGA LETGIE LIK HLV

UniProtKB: Intrinsic membrane protein PufX

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Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 32 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #9: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 9 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #10: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 10 / Number of copies: 3 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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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: 13 / 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: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 12 / Number of copies: 10 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

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Macromolecule #13: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 13 / Number of copies: 25 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #14: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 4 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #16: (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~...

MacromoleculeName: (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
type: ligand / ID: 16 / Number of copies: 27 / Formula: A1EF2
Molecular weightTheoretical: 538.889 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: 50.61 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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