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- EMDB-30656: Structure of RC-LH1-PufX from Rhodobacter veldkampii -

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Basic information

Entry
Database: EMDB / ID: EMD-30656
TitleStructure of RC-LH1-PufX from Rhodobacter veldkampii
Map data
Sample
  • Complex: Photosynthetic core complex featuring reaction center, LH1 and PufX
    • Protein or peptide: x 4 types
  • Protein or peptide: x 2 types
  • Ligand: x 6 types
Keywordsmembrane protein / light-harvesting / reaction center / pufx / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / 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. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex ...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. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / 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
Antenna pigment protein beta chain / Reaction center protein M chain / Uncharacterized protein / Photosynthetic reaction center subunit H / Antenna pigment protein alpha chain / Photosynthetic reaction center L subunit
Similarity search - Component
Biological speciesRhodobacter veldkampii DSM 11550 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsBracun L / Yamagata A
Funding support United Kingdom, Japan, 5 items
OrganizationGrant numberCountry
Royal Society180030 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)R003890 United Kingdom
Japan Agency for Medical Research and Development (AMED)JP20am0101082 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101115 Japan
Japan Society for the Promotion of Science (JSPS)JP 19H03162 Japan
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution.
Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Lu-Ning Liu /
Abstract: The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for ...The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo-electron microscopy structure of the RC-LH1-PufX supercomplex from at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular "cross brace" to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation.
History
DepositionOct 29, 2020-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0157
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0157
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ddq
  • Surface level: 0.0157
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30656.png

Downloads & links

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Map

FileDownload / File: emd_30656.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.0157 / Movie #1: 0.0157
Minimum - Maximum-0.027969923 - 0.06194027
Average (Standard dev.)0.00032288628 (±0.0032009531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z215.800215.800215.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0280.0620.000

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Supplemental data

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Mask #1

Fileemd_30656_msk_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 : Photosynthetic core complex featuring reaction center, LH1 and PufX

EntireName: Photosynthetic core complex featuring reaction center, LH1 and PufX
Components
  • Complex: Photosynthetic core complex featuring reaction center, LH1 and PufX
    • Protein or peptide: PufX
    • Protein or peptide: Photosynthetic reaction center L subunit
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Photosynthetic reaction center subunit HPhotosynthetic reaction centre
  • Protein or peptide: Antenna pigment protein alpha chainPhotosynthetic pigment
  • Protein or peptide: Antenna pigment protein beta chainPhotosynthetic pigment
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: SPHEROIDENE
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: FE (III) ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Photosynthetic core complex featuring reaction center, LH1 and PufX

SupramoleculeName: Photosynthetic core complex featuring reaction center, LH1 and PufX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#6
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)

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Macromolecule #1: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 6.699024 KDa
SequenceString:
MSKFYKIWLI FDPRRVFVAQ GVFLFLLAVM IHLMLLSNPG FNWLDISGVK YERVAAE

UniProtKB: Antenna pigment protein alpha chain

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Macromolecule #2: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 5.551439 KDa
SequenceString:
MADKDLSFTG LTDQQAQELH SVYLQGMWLF ISVAIVAHLA VFIWRPWL

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #3: PufX

MacromoleculeName: PufX / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 8.923259 KDa
SequenceString:
MAEKHYLDGA TKVGMATMGA AAMGKGMGIT AVVFFGTVFF VVALAFIGQF LPDRSREAPY PNTIFQVNDI DGTVDGKYTR FAN

UniProtKB: Uncharacterized protein

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Macromolecule #4: Photosynthetic reaction center L subunit

MacromoleculeName: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 30.896777 KDa
SequenceString: MALLSFERKY RVPGGTLIGG NLFDFWVGPF YVGFFGVTSV FFAALGTLMI LWGASLGDTW NPLLISINPP PLEYGLGAAP LREGGIWQV VTLCAIGAFV SWAMREVEIC RKLGIGLHIP FAFSFAIFAY ITLVVIRPAL MGAWGHGFQY GVFTHLEWVN N VGYQYGNF ...String:
MALLSFERKY RVPGGTLIGG NLFDFWVGPF YVGFFGVTSV FFAALGTLMI LWGASLGDTW NPLLISINPP PLEYGLGAAP LREGGIWQV VTLCAIGAFV SWAMREVEIC RKLGIGLHIP FAFSFAIFAY ITLVVIRPAL MGAWGHGFQY GVFTHLEWVN N VGYQYGNF HYNPLHMLGI SLFFTTTLAL GLHGALILSA ANPETGKEMR TPDHEDTFFR DLVGYSVGTL GIHRLGLLLA LN AAFWSAM CILASGTVWF DQWVFWWDWW YNLPFWADL

UniProtKB: Photosynthetic reaction center L 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: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 34.425746 KDa
SequenceString: MAEYQNIFTQ VQVAGKPELG MVEGVNLENR TTGTTNWPIL GWFGNAQLGP IYLGTLGTMS LIFGAFWFFL VGVSFIIQAD YSPALFLRE LFRAGLFPPA PEYGLSLSAP LMEGGLWLIA SFFLMLSVLL WWARTYKRAA DLGMGKHTAW AFAGALWLMF V LSFFRPIL ...String:
MAEYQNIFTQ VQVAGKPELG MVEGVNLENR TTGTTNWPIL GWFGNAQLGP IYLGTLGTMS LIFGAFWFFL VGVSFIIQAD YSPALFLRE LFRAGLFPPA PEYGLSLSAP LMEGGLWLIA SFFLMLSVLL WWARTYKRAA DLGMGKHTAW AFAGALWLMF V LSFFRPIL MGSWSEAVPY GIFPHLDWTN NFSLTHGNLF YNPFHGLSIA FLYGSTMLFA MHGATILAVS RLGGERELEQ IV DRGTAAE RAALFWRWTM GFNATMEGIH RWGWWFAVLT PVTGGIGILL SGTVVEDWSV WAQVHGYKAL N

UniProtKB: Reaction center protein M chain

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Macromolecule #6: Photosynthetic reaction center subunit H

MacromoleculeName: Photosynthetic reaction center subunit H / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Molecular weightTheoretical: 27.445557 KDa
SequenceString: MVGVNFFGDF DLASLAIWSF WLFFALLVYY LQTENMREGY PLENEDGGPA VNQGPFPLPS QKTFKLPHGR GEVTVPDYKK EARDVALAR TAVNDGFPHA PTGNPMLDGV GPASWAPRRD IPELDGHGHA KVVPMSVASA FFVSAGRDPR GLPVIANDMK T VGTVTEMW ...String:
MVGVNFFGDF DLASLAIWSF WLFFALLVYY LQTENMREGY PLENEDGGPA VNQGPFPLPS QKTFKLPHGR GEVTVPDYKK EARDVALAR TAVNDGFPHA PTGNPMLDGV GPASWAPRRD IPELDGHGHA KVVPMSVASA FFVSAGRDPR GLPVIANDMK T VGTVTEMW VDVAEHMVRY LEVDLASGGK CLVPMTMAII KKHAVVVQSI SSAAFASVPQ TKSMTEISML EEEKICAYFA GG TMYCADA KPKLF

UniProtKB: Photosynthetic reaction center subunit H

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 34 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #8: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 8 / Number of copies: 15 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #9: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 9 / Number of copies: 6 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #10: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 10 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #11: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #12: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 12 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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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 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184921
FSC plot (resolution estimation)

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