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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 / 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, 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 / PRC-barrel-like superfamily / Photosynthetic reaction centre, L subunit / : / 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: Photosynth Res / Year: 2025
Title: Molecular and structural insights into neurosporene accumulation in Rhodobacter sphaeroides G1C.
Authors: Yu-Lu Wu / Guang-Lei Wang / Xiang-Ping Wang / Xing-Yu Yue / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Richard J Cogdell / Long-Jiang Yu /
Abstract: Carotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid ...Carotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid neurosporene, a key intermediate in carotenoid biosynthesis, plays a central role in the production of several other carotenoids; however, neurosporene accumulation is rare in nature. In this study, we investigated the accumulation of neurosporene in Rhodobacter sphaeroides strain G1C, a mutant derivative of wild-type Rba. sphaeroides 2.4.1 obtained by nitrosoguanidine mutagenesis. Whole-genome sequencing of strain G1C identified a nonsense mutation in the crtC gene resulting in enzyme inactivation and disruption of normal carotenoid biosynthesis. Physiological analysis and cryo-EM structural analysis of the major photosynthetic complexes of strain G1C showed that the accumulation of neurosporene did not significantly alter either the structure or functioning of the light-harvesting complexes and had no perceptible effect on photosynthetic growth. While the carotenoid composition of strain G1C shifts from spheroidene to neurosporene, its photocomplexes remain structurally intact and their physiological properties remain largely unchanged. This study provides genomic insights into the importance of CrtC activity to the production of carotenoids in Rba. sphaeroides and highlights the unexpected finding that carotenoid substitution in photocomplexes can occur without significantly disrupting photocomplex function.
History
DepositionNov 14, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing 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
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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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