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- EMDB-63382: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercompl... -

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Entry
Database: EMDB / ID: EMD-63382
TitleCryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
Map data
Sample
  • Complex: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
    • Protein or peptide: x 7 types
  • Ligand: x 6 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 / metal ion binding / 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, 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 / PRC-barrel-like superfamily / Photosynthetic reaction centre, L subunit / 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: 2.75 Å
AuthorsLiu ZK / Wang P / Liu LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370136 China
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis for aerobic anoxygenic photosynthesis in the reaction center-light-harvesting 1 (RC-LH1) supercomplex of Dinoroseobacter shibae.
Authors: Ze-Kun Liu / Jian-Xun Li / Ying-Yue Zhang / Jing-Li Lv / Kang Li / Xiu-Lan Chen / Yu-Zhong Zhang / Lu-Ning Liu / Peng Wang /
Abstract: Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, their architecture and structural adaptations of their photosynthetic systems to ensure adequate ...Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, their architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present a 2.4-Å cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 αβ-subunits, each containing two spheroidenones per αβ-heterodimer-a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, which may account for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown subunit, protein-LRC, which is hypothesized to functionally couple photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.
History
DepositionFeb 6, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63382.png

Downloads & links

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Map

FileDownload / File: emd_63382.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1717991 - 1.9839053
Average (Standard dev.)0.0020757862 (±0.060132317)
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_63382_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #1

Fileemd_63382_half_map_2.map
Projections & Slices
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Sample components

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

EntireName: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
Components
  • Complex: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Protein LRC
    • 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: BACTERIOCHLOROPHYLL A
  • Ligand: SPEROIDENONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-10
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: FE (III) ION

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

SupramoleculeName: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
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: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 14 / 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 #2: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 14 / 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: Protein LRC

MacromoleculeName: Protein LRC / type: protein_or_peptide / ID: 3 / 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 #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: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 32 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #9: SPEROIDENONE

MacromoleculeName: SPEROIDENONE / type: ligand / ID: 9 / Number of copies: 27 / Formula: SPN
Molecular weightTheoretical: 594.993 Da
Chemical component information

ChemComp-SPN:
SPEROIDENONE

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / 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 #11: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 11 / Number of copies: 3 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #12: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 12 / Number of copies: 3 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

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Macromolecule #13: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 13 / 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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44589
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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44589
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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