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- EMDB-32047: Rba sphaeroides WT RC-LH1 monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-32047
TitleRba sphaeroides WT RC-LH1 monomer
Map data
Sample
  • Complex: Rhodobacter sphaeroides WT RC-LH1 monomer
    • Protein or peptide: x 7 types
  • Ligand: x 7 types
KeywordsComplex / 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 / : / photosynthesis / membrane / 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, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / 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
Intrinsic membrane protein PufX / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain / Uncharacterized protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria) / Cereibacter sphaeroides 2.4.1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsBracun L / Yamagata A / Liu LN / Shirouzu M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Authors: Peng Cao / Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tatsuki Negami / Baohua Zou / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Mei Li / Lu-Ning Liu /
Abstract: The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species ...The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.
History
DepositionOct 12, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32047.png

Downloads & links

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Map

FileDownload / File: emd_32047.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.18242697 - 0.29518566
Average (Standard dev.)0.00007773828 (±0.014516941)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_32047_additional_1.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 : Rhodobacter sphaeroides WT RC-LH1 monomer

EntireName: Rhodobacter sphaeroides WT RC-LH1 monomer
Components
  • Complex: Rhodobacter sphaeroides WT RC-LH1 monomer
    • 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: Light-harvesting protein B-875 beta chain
    • Protein or peptide: Intrinsic membrane protein PufX
    • Protein or peptide: Rsp_7571 Protein-Y PufY
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN B
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: UBIQUINONE-10
  • Ligand: FE (II) ION
  • Ligand: SPHEROIDENE
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Rhodobacter sphaeroides WT RC-LH1 monomer

SupramoleculeName: Rhodobacter sphaeroides WT RC-LH1 monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Rhodobacter sphaeroides 2.4.1 (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 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 31.477584 KDa
SequenceString: MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGLGGAP LAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLDWVS N TGYTYGNF ...String:
MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGLGGAP LAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLDWVS N TGYTYGNF HYNPAHMIAI SFFFTNALAL ALHGALVLSA ANPEKGKEMR TPDHEDTFFR DLVGYSIGTL GIHRLGLLLS LS AVFFSAL 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 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 34.529738 KDa
SequenceString: MAEYQNIFSQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFWYQAG WNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIWLWM V LGFIRPIL ...String:
MAEYQNIFSQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFWYQAG WNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIWLWM V LGFIRPIL MGSWSEAVPY GIFSHLDWTN NFSLVHGNLF YNPFHGLSIA FLYGSALLFA MHGATILAVS RFGGERELEQ IA DRGTAAE 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 2.4.1 (bacteria) / Strain: 2.4.1.
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 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 6.816169 KDa
SequenceString:
MSKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRVAVAE

UniProtKB: Light-harvesting protein B-875 alpha chain

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Macromolecule #5: Light-harvesting protein B-875 beta chain

MacromoleculeName: Light-harvesting protein B-875 beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 5.592361 KDa
SequenceString:
MADKSDLGYT GLTDEQAQEL HSVYMSGLWL FSAVAIVAHL AVYIWRPWF

UniProtKB: Light-harvesting protein B-875 beta chain

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Macromolecule #6: Intrinsic membrane protein PufX

MacromoleculeName: Intrinsic membrane protein PufX / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 9.061646 KDa
SequenceString:
MADKTIFNDH LNTNPKTNLR LWVAFQMMKG AGWAGGVFFG TLLLIGFFRV VGRMLPIQEN QAPAPNITGA LETGIELIKH LV

UniProtKB: Intrinsic membrane protein PufX

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Macromolecule #7: Rsp_7571 Protein-Y PufY

MacromoleculeName: Rsp_7571 Protein-Y PufY / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1.
Molecular weightTheoretical: 5.555558 KDa
SequenceString:
MPEVSEFAFR LMMAAVIFVG VGIMFAFAGG HWFVGLVVGG LVAAFFAATP NSN

UniProtKB: Uncharacterized protein

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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 B

MacromoleculeName: BACTERIOPHEOPHYTIN B / type: ligand / ID: 9 / Number of copies: 2 / Formula: BPB
Molecular weightTheoretical: 887.199 Da
Chemical component information

ChemComp-BPB:
BACTERIOPHEOPHYTIN B

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Macromolecule #10: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 10 / Number of copies: 9 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #11: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 11 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #12: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #13: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 13 / Number of copies: 26 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / 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
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.026 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68554
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion
FSC plot (resolution estimation)

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