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- EMDB-63379: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-63379
TitleCryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
Map data
Sample
  • Complex: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
    • Protein or peptide: x 7 types
  • Ligand: x 7 types
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 transfer activity / iron ion binding / heme binding ...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 transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome 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
Uncharacterized protein / Antenna pigment protein beta chain / Antenna pigment protein alpha chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit / Reaction center protein H chain
Similarity search - Component
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsLiu ZK / Wang P / Liu LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370136 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
Authors: Liu ZK / Wang P / Liu LN
History
DepositionFeb 6, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63379.png

Downloads & links

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Map

FileDownload / File: emd_63379.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291. Å		0.97 Å/pix.
x 300 pix.
= 291. Å		0.97 Å/pix.
x 300 pix.
= 291. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.96817464 - 2.0721948
Average (Standard dev.)0.0028049052 (±0.062235236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63379_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_63379_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex

EntireName: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
Components
  • Complex: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
    • Protein or peptide: Protein LRC
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • Protein or peptide: Reaction center protein H chain
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
  • Ligand: UBIQUINONE-10
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: SPEROIDENONE
  • Ligand: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: FE (III) ION

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Supramolecule #1: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex

SupramoleculeName: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

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Macromolecule #1: Protein LRC

MacromoleculeName: Protein LRC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 7.963479 KDa
SequenceString:
DMTCTITCWG IGVLLGIMTT VGLMVVGWSF LQGAFMGVLA WLIVGGVLAV AVCGKDNAEQ IRAEMAAARE RVRGAT

UniProtKB: Uncharacterized protein

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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: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 5.993136 KDa
SequenceString:
MSKFYKIWLI FDPRRVFVAQ GVFLFLLAAM IHLVLLSTEH FNWFELAAAN A

UniProtKB: Antenna pigment protein alpha chain

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Macromolecule #3: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 5.044715 KDa
SequenceString:
DLSFTGLTDE QAQELHSVYM SGLWLFSAVA VVAHLATFIW RPWF

UniProtKB: Antenna pigment protein beta chain

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Macromolecule #4: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 39.580883 KDa
SequenceString: KWFDEWNSKN PTDIYKPAIV VGVAGGAVFA AALLVSMGQP LATDSMQTGP RGTGMSVPEF VSDLDTPDPT IEVFLASTSD PVIPEEGAQ TAGEAYENVD PVLADLTVEN YDRLLAAMRS WTGIPDLLED PDHYQSKVAI NMIQMNQTIN EEWAGHVYAN A EVGVTCFT ...String:
KWFDEWNSKN PTDIYKPAIV VGVAGGAVFA AALLVSMGQP LATDSMQTGP RGTGMSVPEF VSDLDTPDPT IEVFLASTSD PVIPEEGAQ TAGEAYENVD PVLADLTVEN YDRLLAAMRS WTGIPDLLED PDHYQSKVAI NMIQMNQTIN EEWAGHVYAN A EVGVTCFT CHRGQAVPSE VWYRIDPVTE NTSGWASVQN RATSLSQFTS LPSDALYQYL LNYEQIAVHD LESRVETLPG DP TWQNTER TYSLMNYFSN SLGRNCVFCH NSRAFYDPAQ HTPQWATAML GISMVQELNN EWIVPIGEAH LPPERLGPVY NDV PKLACK TCHKGYQQPL QGLNVVADWP ELATTEGPFY D

UniProtKB: Photosynthetic reaction center cytochrome c subunit

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Macromolecule #5: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 28.621299 KDa
SequenceString: EETFFGNFDL ASLSLWLFYG FFALLIYYLQ TENMREGYPL EDEDGNTAAN QGPFPLPKEK TFKLQHGRGE LTLPGEDVQR RDNLALRKT AHGNGFPMEP TGDPMLDGVG PASWSKRRDV PELDAHGHPK IVPMSAAEGF GVSAGTDPRG LPVMAGDGEI V GLVSDMWI ...String:
EETFFGNFDL ASLSLWLFYG FFALLIYYLQ TENMREGYPL EDEDGNTAAN QGPFPLPKEK TFKLQHGRGE LTLPGEDVQR RDNLALRKT AHGNGFPMEP TGDPMLDGVG PASWSKRRDV PELDAHGHPK IVPMSAAEGF GVSAGTDPRG LPVMAGDGEI V GLVSDMWI DEAEQLVRYL ELELDPEWGD GKRLVQRQMV RIKSDRVKVR SIYGKHFKNV PKTKSPNQVT LLEEDKIMAY YA GGTLYAD ESRLEPQL

UniProtKB: Reaction center protein H chain

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Macromolecule #6: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 30.533416 KDa
SequenceString: ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTAF FALLGTILIF WGASQQGTFN PWLINIAPPD LSYGLGMAPL MEGGLWQII TICAIGAFVS WALREVEICR KLGMGYHVPF AFSVAIFAYV TLVVFRPLLM GAWGHGFPYG IWSHLDWVSN T GYAYLHFH ...String:
ALLSFERKYR VRGGTLIGGD LFDFWVGPFY VGFFGVTTAF FALLGTILIF WGASQQGTFN PWLINIAPPD LSYGLGMAPL MEGGLWQII TICAIGAFVS WALREVEICR KLGMGYHVPF AFSVAIFAYV TLVVFRPLLM GAWGHGFPYG IWSHLDWVSN T GYAYLHFH YNPAHMLAVT FFFTTTLALA LHGALVLSAA NPPKGEEVKG PDNEDTFFRD FIGYSIGTLG IHRVGLLLAL NA GFWSAVC IIISGPVWTK GWPEWWNWWL EMPIWP

UniProtKB: Reaction center protein L chain

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Macromolecule #7: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 37.037172 KDa
SequenceString: PEYQNIFTQV QVQGPAELGV DNENNLTEER TTGTGFSQLI GWIGNAQLGP IYLGWFGIIS LVTGTLWFNI VGFNMLSQVG YSIPEFIRQ LFWLALEPPS PEYGLRMPPL DDGGWFIIAS FFLLVSVISW WLRTYQLAEM HKMGKHVAWA FAAAIWLFLV L GLFRPILM ...String:
PEYQNIFTQV QVQGPAELGV DNENNLTEER TTGTGFSQLI GWIGNAQLGP IYLGWFGIIS LVTGTLWFNI VGFNMLSQVG YSIPEFIRQ LFWLALEPPS PEYGLRMPPL DDGGWFIIAS FFLLVSVISW WLRTYQLAEM HKMGKHVAWA FAAAIWLFLV L GLFRPILM GSWSEAVPYG IFPHLDWTTA FSIRYGNLYY NPFHALSIVF LYGSVLLFAM HGATILAVTR FGGDRELEQI YD RGTASER AGLFWRWTMG FNATMEGIHR WAWWFAVLTP ITGGIGILLT GTVVDNWFLW AVEHNFAPDY TQDYGYEAYT TYD GFLGR

UniProtKB: Reaction center protein M chain

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Macromolecule #8: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 8 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 38 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #10: SPEROIDENONE

MacromoleculeName: SPEROIDENONE / type: ligand / ID: 10 / Number of copies: 35 / Formula: SPN
Molecular weightTheoretical: 594.993 Da
Chemical component information

ChemComp-SPN:
SPEROIDENONE

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Macromolecule #11: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24l...

MacromoleculeName: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
type: ligand / ID: 11 / Number of copies: 9 / Formula: MW9
Molecular weightTheoretical: 777.06 Da
Chemical component information

ChemComp-MW9:
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate

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Macromolecule #12: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 12 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #13: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 13 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #14: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
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

MicroscopeTFS 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: 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 #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6et5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123390
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6et5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123390
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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