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- EMDB-62025: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62025
TitleCryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Map data
Sample
  • Complex: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
    • Protein or peptide: Light-harvesting protein B-870 beta chain
    • Protein or peptide: Light-harvesting protein B-870 alpha chain
    • Protein or peptide: Photoreaction center protein H
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
  • Ligand: SPIRILLOXANTHIN
  • Ligand: FE (III) ION
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10
Keywordsreaction centre light-harvesting 1 / 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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 ...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
Light-harvesting protein B-870 alpha chain / Light-harvesting protein B-870 beta chain / 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: 3.02 Å
AuthorsLiu ZK / Wang P / Liu LN
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Authors: Liu ZK / Wang P / Liu LN
History
DepositionOct 19, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62025.png

Downloads & links

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Map

FileDownload / File: emd_62025.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: 0.15
Minimum - Maximum-0.6665557 - 1.2670763
Average (Standard dev.)0.009040664 (±0.045457553)
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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Half map: #2

Fileemd_62025_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_62025_half_map_2.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 : reaction center_light harvesting complex 1 from Rhodospirillum rubrum

EntireName: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
Components
  • Complex: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
    • Protein or peptide: Light-harvesting protein B-870 beta chain
    • Protein or peptide: Light-harvesting protein B-870 alpha chain
    • Protein or peptide: Photoreaction center protein H
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
  • Ligand: SPIRILLOXANTHIN
  • Ligand: FE (III) ION
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10

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Supramolecule #1: reaction center_light harvesting complex 1 from Rhodospirillum rubrum

SupramoleculeName: reaction center_light harvesting complex 1 from Rhodospirillum rubrum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

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Macromolecule #1: Light-harvesting protein B-870 beta chain

MacromoleculeName: Light-harvesting protein B-870 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 5.037832 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum (bacteria)
SequenceString:
ITEGEAKEFH KIFTSSILVF FGVAAFAHLL VWIWRPWVPG PNGY

UniProtKB: Light-harvesting protein B-870 beta chain

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Macromolecule #2: Light-harvesting protein B-870 alpha chain

MacromoleculeName: Light-harvesting protein B-870 alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 5.308227 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum (bacteria)
SequenceString:
WRIWQLFDPR QALVGLATFL FVLALLIHFI LLSTERFNWL EGAST

UniProtKB: Light-harvesting protein B-870 alpha 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: 27.745863 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum (bacteria)
SequenceString: NKGDITGYMD VAQVVLYAFW IFFAGLIIYL RREDRREGYP LEDAISGKIN SLQGLGSVFS IARPKIFKLK TGATYAAPNF KRDAVAIKA TRTAPTAGAP FEPTGNPMTD AVGPAAYALR DELPDLTLGG QPAIVPLRVA PTFSVAAEDT DPRGLPVVDR K GAVAGKVT ...String:
NKGDITGYMD VAQVVLYAFW IFFAGLIIYL RREDRREGYP LEDAISGKIN SLQGLGSVFS IARPKIFKLK TGATYAAPNF KRDAVAIKA TRTAPTAGAP FEPTGNPMTD AVGPAAYALR DELPDLTLGG QPAIVPLRVA PTFSVAAEDT DPRGLPVVDR K GAVAGKVT DLWIDRASIA IRYLEVELAA TPGRKVLLPF AATRINAKTK SKTVTVQSIL ARHFANVPTI AKTDSITRRE ED KVMAYYS SGYLYSDR

UniProtKB: Photoreaction center protein 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: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 30.472436 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum (bacteria)
SequenceString: ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTLL FTVLGTALIV WGAALGPSWT FWQISINPPD VSYGLAMAPM AKGGLWQII TFSAIGAFVS WALREVEICR KLGIGYHIPF AFGFAILAYV SLVVIRPVMM GAWGYGFPYG FMTHLDWVSN T GYQYANFH ...String:
ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTLL FTVLGTALIV WGAALGPSWT FWQISINPPD VSYGLAMAPM AKGGLWQII TFSAIGAFVS WALREVEICR KLGIGYHIPF AFGFAILAYV SLVVIRPVMM GAWGYGFPYG FMTHLDWVSN T GYQYANFH YNPAHMLGIT LFFTTCLALA LHGSLILSAA NPGKGEVVKG PEHENTYFQD TIGYSVGTLG IHRVGLILAL SA VVWSIIC MILSGPIYTG SWPDWWLWWQ KLPFWNH

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: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 29.131648 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum (bacteria)
SequenceString: GPIYLGTTGV LSLVFGFFAI EIIGFNLLAS VNWSPMEFGR QFFWLGLEPP AAEYGLGFAP LAEGGWWQIA GFFLTTSILL WWVRMYRRA RALKMGTHTA WAFASAIFLF LSLGFIRPLL MGNFSESVPF GIFPHLEWTN SFSLNYGNFF YNPFHMLSIA F LYGSALLF ...String:
GPIYLGTTGV LSLVFGFFAI EIIGFNLLAS VNWSPMEFGR QFFWLGLEPP AAEYGLGFAP LAEGGWWQIA GFFLTTSILL WWVRMYRRA RALKMGTHTA WAFASAIFLF LSLGFIRPLL MGNFSESVPF GIFPHLEWTN SFSLNYGNFF YNPFHMLSIA F LYGSALLF AMHGATILAV SRLGGDREVE QITDRGTAAE RAALFWRWTM GFNATMESIH RWAWWFAVLC TFTGAIGILL TG TVVDNWF EWGVKHGLAP AP

UniProtKB: Reaction center protein M chain

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Macromolecule #6: Trans-Geranyl BACTERIOCHLOROPHYLL A

MacromoleculeName: Trans-Geranyl BACTERIOCHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 37 / Formula: 07D
Molecular weightTheoretical: 901.425 Da
Chemical component information

ChemComp-07D:
Trans-Geranyl BACTERIOCHLOROPHYLL A

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Macromolecule #7: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 7 / Number of copies: 17 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #8: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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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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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: PDB ENTRY
PDB model - PDB ID:

7oy8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97584
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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