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- EMDB-62663: Cryo-EM structure of the RC complex from Rhodospirillum rubrum -

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Basic information

Entry
Database: EMDB / ID: EMD-62663
TitleCryo-EM structure of the RC complex from Rhodospirillum rubrum
Map data
Sample
  • Complex: RC COMPLEX
    • Protein or peptide: x 3 types
  • Ligand: x 11 types
Keywordslight harvesting / photosynthesis / gene heterologous expression / Rhodospirillum rubrum / STRUCTURAL PROTEIN
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
Similarity search - Function
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 / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily ...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 / 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 / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang L / Yu L-J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC341800 China
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Assembly, selectivity, and compatibility of bacterial photosynthetic complexes from divergent species detected in a chimeric strain.
Authors: Lu Wang / Yi-Hao Yan / Guang-Lei Wang / Xing-Yu Yue / Chen-Hui Qi / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Yueyong Xin / Long-Jiang Yu /
Abstract: Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein ...Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein structures is a topic of great interest, and assembly mechanisms appear to reflect the evolutionary diversity of the particular phototrophic organism. Here we constructed a photosynthetic chimera expressing the Roseiflexus castenholzii LH and Rhodospirillum rubrum RC complexes in a photocomplex-deficient Rsp. rubrum mutant, and spectroscopy confirmed LH expression with absorption maxima at 878 and 801 nm. The chimeric strain grew slower phototrophically than wildtype but faster than a strain containing only the RC, indicating partial energy transfer from LH to RC. Cryo-EM structural analysis revealed that the Rfl. castenholzii LH independently assembled into a closed ring of 15 αβ heterodimers lacking carotenoids, resulting in a blue-shifted Q transition, while the Rsp. rubrum RC formed a separate complex with an RC:LH ratio of ∼17:1 instead of a typical 1:1. Structural differences, including the absence of two Rfl. castenholzii-specific small proteins, likely precluded formation of a conjoined LH-RC in the chimeric strain. These results reveal that distinct photocomplex assembly strategies exist in phylogenetically divergent species and underscore the modularity and adaptability of photosynthetic complexes, offering insights for artificial photosystem design.
History
DepositionDec 10, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62663.png

Downloads & links

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Map

FileDownload / File: emd_62663.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: 0.192
Minimum - Maximum-1.0770931 - 1.8122839
Average (Standard dev.)-0.000040769424 (±0.026885504)
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: #1

Fileemd_62663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62663_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 : RC COMPLEX

EntireName: RC COMPLEX
Components
  • Complex: RC COMPLEX
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Photoreaction center protein H
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
  • Ligand: Trans-Geranyl 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: DODECYL-BETA-D-MALTOSIDE
  • Ligand: Octadecane
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: FE (III) ION
  • Ligand: SPIRILLOXANTHIN
  • Ligand: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
  • Ligand: CARDIOLIPIN

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Supramolecule #1: RC COMPLEX

SupramoleculeName: RC COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rhodospirillum rubrum (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: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 30.660688 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTL LFTVLGTALI VWGAALGPSW TFWQISINPP DVSYGLAMAP MAKGGLWQI ITFSAIGAFV SWALREVEIC RKLGIGYHIP FAFGFAILAY VSLVVIRPVM MGAWGYGFPY GFMTHLDWVS N TGYQYANF ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTL LFTVLGTALI VWGAALGPSW TFWQISINPP DVSYGLAMAP MAKGGLWQI ITFSAIGAFV SWALREVEIC RKLGIGYHIP FAFGFAILAY VSLVVIRPVM MGAWGYGFPY GFMTHLDWVS N TGYQYANF HYNPAHMLGI TLFFTTCLAL ALHGSLILSA ANPGKGEVVK GPEHENTYFQ DTIGYSVGTL GIHRVGLILA LS AVVWSII CMILSGPIYT GSWPDWWLWW QKLPFWNHG

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: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 34.234547 KDa
SequenceString: MSEYQNILTG VQVRTAPHSA PIAKGIFPRL GKPGFSYWLG KIGDAQIGPI YLGTTGVLSL VFGFFAIEII GFNLLASVNW SPMEFGRQF FWLGLEPPAA EYGLGFAPLA EGGWWQIAGF FLTTSILLWW VRMYRRARAL KMGTHTAWAF ASAIFLFLSL G FIRPLLMG ...String:
MSEYQNILTG VQVRTAPHSA PIAKGIFPRL GKPGFSYWLG KIGDAQIGPI YLGTTGVLSL VFGFFAIEII GFNLLASVNW SPMEFGRQF FWLGLEPPAA EYGLGFAPLA EGGWWQIAGF FLTTSILLWW VRMYRRARAL KMGTHTAWAF ASAIFLFLSL G FIRPLLMG NFSESVPFGI FPHLEWTNSF SLNYGNFFYN PFHMLSIAFL YGSALLFAMH GATILAVSRL GGDREVEQIT DR GTAAERA ALFWRWTMGF NATMESIHRW AWWFAVLCTF TGAIGILLTG TVVDNWFEWG VKHGLAPAP

UniProtKB: Reaction center protein M chain

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Macromolecule #3: Photoreaction center protein H

MacromoleculeName: Photoreaction center protein H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 27.976193 KDa
SequenceString: MNKGDITGYM DVAQVVLYAF WIFFAGLIIY LRREDRREGY PLEDAISGKI NSLQGLGSVF SIARPKIFKL KTGATYAAPN FKRDAVAIK ATRTAPTAGA PFEPTGNPMT DAVGPAAYAL RDELPDLTLG GQPAIVPLRV APTFSVAAED TDPRGLPVVD R KGAVAGKV ...String:
MNKGDITGYM DVAQVVLYAF WIFFAGLIIY LRREDRREGY PLEDAISGKI NSLQGLGSVF SIARPKIFKL KTGATYAAPN FKRDAVAIK ATRTAPTAGA PFEPTGNPMT DAVGPAAYAL RDELPDLTLG GQPAIVPLRV APTFSVAAED TDPRGLPVVD R KGAVAGKV TDLWIDRASI AIRYLEVELA ATPGRKVLLP FAATRINAKT KSKTVTVQSI LARHFANVPT IAKTDSITRR EE DKVMAYY SSGYLYSDRV

UniProtKB: Photoreaction center protein H

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Macromolecule #4: Trans-Geranyl BACTERIOCHLOROPHYLL A

MacromoleculeName: Trans-Geranyl BACTERIOCHLOROPHYLL A / type: ligand / ID: 4 / Number of copies: 4 / Formula: 07D
Molecular weightTheoretical: 901.425 Da
Chemical component information

ChemComp-07D:
Trans-Geranyl BACTERIOCHLOROPHYLL A

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Macromolecule #5: Trans-Geranyl BACTERIOPHEOPHYTIN A

MacromoleculeName: Trans-Geranyl BACTERIOPHEOPHYTIN A / type: ligand / ID: 5 / Number of copies: 2 / Formula: 08I
Molecular weightTheoretical: 879.136 Da
Chemical component information

ChemComp-08I:
Trans-Geranyl BACTERIOPHEOPHYTIN A

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Macromolecule #6: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 6 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #7: (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: 7 / Number of copies: 20 / 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 #8: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #9: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 9 / Number of copies: 7 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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Macromolecule #10: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 10 / Number of copies: 5 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 12 / Number of copies: 1 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #13: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E}...

MacromoleculeName: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6- ...Name: 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
type: ligand / ID: 13 / Number of copies: 1 / Formula: RQ0
Molecular weightTheoretical: 844.3 Da
Chemical component information

ChemComp-RQ0:
2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione

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Macromolecule #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 1 / 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: 7.5
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: 60.24 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: PDB ENTRY
PDB model - PDB ID:

7eqd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 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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