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- EMDB-39244: Rhodobacter blasticus RC-LH1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-39244
TitleRhodobacter blasticus RC-LH1 dimer
Map data
Sample
  • Complex: Rhodobacter blasticus RC-LH1 dimer
    • Protein or peptide: x 6 types
  • Ligand: x 7 types
Keywordsphotosynthesis / light-harvesting complex
Function / homology
Function and homology information


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/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / 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/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
Reaction center protein L chain / Photosynthetic reaction center subunit H / Reaction center protein M chain / 1-deoxy-D-xylulose-5-phosphate synthase / Antenna pigment protein alpha chain / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesFuscovulum blasticum DSM 2131 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLiu LN / Zhang YZ / Wang P / Christianson BM / Ugurlar D
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32170127 China
CitationJournal: Sci Adv / Year: 2024
Title: Architectures of photosynthetic RC-LH1 supercomplexes from .
Authors: Peng Wang / Bern M Christianson / Deniz Ugurlar / Ruichao Mao / Yi Zhang / Ze-Kun Liu / Ying-Yue Zhang / Adrian M Gardner / Jun Gao / Yu-Zhong Zhang / Lu-Ning Liu /
Abstract: The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric ...The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from () using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike counterpart, RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome . Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.
History
DepositionFeb 26, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39244.png

Downloads & links

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Map

FileDownload / File: emd_39244.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 237.824 Å		0.93 Å/pix.
x 256 pix.
= 237.824 Å		0.93 Å/pix.
x 256 pix.
= 237.824 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.929 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.76836497 - 1.1767334
Average (Standard dev.)0.0050674095 (±0.08246518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 237.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39244_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39244_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rhodobacter blasticus RC-LH1 dimer

EntireName: Rhodobacter blasticus RC-LH1 dimer
Components
  • Complex: Rhodobacter blasticus RC-LH1 dimer
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Photosynthetic reaction center subunit H
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: SPHEROIDENE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CARDIOLIPIN
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
  • Ligand: FE (II) ION

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Supramolecule #1: Rhodobacter blasticus RC-LH1 dimer

SupramoleculeName: Rhodobacter blasticus RC-LH1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)

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Macromolecule #1: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 5.614452 KDa
SequenceString:
MADKSDLSFT GLSDEQAQEL HSVYMSGLWL FVTIAVIAHI AVYIWRPWL

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #2: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 7.096406 KDa
SequenceString:
MSKFYKIWQV FDPRRVFVAQ GVFLFLLAVM IHLILLSKPD YNWLDVGTAK YGRGEAAAVV TP

UniProtKB: Antenna pigment protein alpha chain

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Macromolecule #3: Photosynthetic reaction center subunit H

MacromoleculeName: Photosynthetic reaction center subunit H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 28.320168 KDa
SequenceString: MVGVNFFGDF DLASLAIWSF WGFLAFLIYY LQTENMREGY PLEMEDGSVA PNQGLFPVPK PKTFKLPNGR GEIVMPSAEN EAAHRRNDL ALARTSVSEG FPHAPTGNAL VDGVGPASWV PRRDEPELDA HGHNKIMPMA LAKGFNVTAG RDPRGLPVQA A DLEVVGRV ...String:
MVGVNFFGDF DLASLAIWSF WGFLAFLIYY LQTENMREGY PLEMEDGSVA PNQGLFPVPK PKTFKLPNGR GEIVMPSAEN EAAHRRNDL ALARTSVSEG FPHAPTGNAL VDGVGPASWV PRRDEPELDA HGHNKIMPMA LAKGFNVTAG RDPRGLPVQA A DLEVVGRV SELWVDVPEQ MVRYLEIDLN SGKKRLVPMT LAKIWADRVR VNAIASDSFE NIPATRSASE VTKLEEDKIS GY VAGGWLY DADKRKRGF

UniProtKB: Photosynthetic reaction center subunit H

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Macromolecule #4: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 31.494471 KDa
SequenceString: MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVTTF FFAALGTLLI LYGTAMEGVW NPQLISIEPP SVENGLAFAP LAEGGLWQL ITICALGAFI SWALREVEIC RKLGIGLHIP FAFSFAILAY AVLVVFRPLL MGSWGYAFPY GIWTHLDWVS N TGYTYGNF ...String:
MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVTTF FFAALGTLLI LYGTAMEGVW NPQLISIEPP SVENGLAFAP LAEGGLWQL ITICALGAFI SWALREVEIC RKLGIGLHIP FAFSFAILAY AVLVVFRPLL MGSWGYAFPY GIWTHLDWVS N TGYTYGNF HYNPAHMLGI SFFFTTALAL ALHGALVLSA ANPEKGQEMK TADHEDTFFR DLVGYSIGTL GIHRLGLLLA LM AVFWSAV CMIITGTIWF DQWSNWWYWW VELPWWVDIP GGVNG

UniProtKB: Reaction center protein L chain

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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: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 34.542602 KDa
SequenceString: MAEYQNIFTQ VQVGGAPEMG LVEGVDLSNR TKGTTNWTLL GWFGNAQIGP IYLGGWGTVS LISGVLWFMT IGAWFWYEAG FNPAVFMRD LFYLSLDAPD AKYGLGVPRD AEGIMWFIAS FFMFVAVWSW WIRTYTRAAA LGMGKHTAWA FLSAIWLWMV L GFIRPILM ...String:
MAEYQNIFTQ VQVGGAPEMG LVEGVDLSNR TKGTTNWTLL GWFGNAQIGP IYLGGWGTVS LISGVLWFMT IGAWFWYEAG FNPAVFMRD LFYLSLDAPD AKYGLGVPRD AEGIMWFIAS FFMFVAVWSW WIRTYTRAAA LGMGKHTAWA FLSAIWLWMV L GFIRPILM GSWSEAVPYG IFTHLDWTNN FSLTYGNLFY NPFHGLSIAF LYGSALLFAM HGATILAVSR FGGDRELEQI VD RGTAAER AALFWRWTMG FNATMEGIHR WAWWFGVLVT LTGGIGILLS GTVVDNWYVW AQVHGYAPVN

UniProtKB: Reaction center protein M chain

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Macromolecule #6: 1-deoxy-D-xylulose-5-phosphate synthase

MacromoleculeName: 1-deoxy-D-xylulose-5-phosphate synthase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fuscovulum blasticum DSM 2131 (bacteria)
Molecular weightTheoretical: 8.046359 KDa
SequenceString:
MAEYNYSHEP NAVINLRVWA LGQMVWGAFL AAVGVVVVIC LLVGTYLAGL LLPEQSKQAP SPYGALEIVQ TIDVA

UniProtKB: 1-deoxy-D-xylulose-5-phosphate synthase

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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

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Macromolecule #8: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 8 / Number of copies: 29 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #9: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 11 / 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 #10: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 10 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #11: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 11 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #12: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 12 / Number of copies: 7 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #13: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9149
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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