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- PDB-9ltv: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercompl... -

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Basic information

Entry
Database: PDB / ID: 9ltv
TitleCryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
  • Protein LRC
KeywordsPHOTOSYNTHESIS / reaction centre light-harvesting 1
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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / SPEROIDENONE / UBIQUINONE-10 / Uncharacterized protein / Antenna pigment protein beta chain / Antenna pigment protein alpha chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / SPEROIDENONE / UBIQUINONE-10 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsLiu, Z.K. / Wang, P. / Liu, L.N.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
2: Antenna pigment protein beta chain
3: Antenna pigment protein alpha chain
4: Antenna pigment protein beta chain
5: Antenna pigment protein alpha chain
6: Antenna pigment protein beta chain
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
9: Antenna pigment protein alpha chain
A: Protein LRC
C: Photosynthetic reaction center cytochrome c subunit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
a: Antenna pigment protein alpha chain
b: Antenna pigment protein beta chain
c: Antenna pigment protein alpha chain
d: Antenna pigment protein beta chain
e: Antenna pigment protein alpha chain
f: Antenna pigment protein beta chain
g: Antenna pigment protein alpha chain
h: Antenna pigment protein beta chain
i: Antenna pigment protein alpha chain
j: Antenna pigment protein beta chain
k: Antenna pigment protein alpha chain
l: Antenna pigment protein beta chain
m: Antenna pigment protein alpha chain
n: Antenna pigment protein beta chain
o: Antenna pigment protein alpha chain
p: Antenna pigment protein beta chain
w: Antenna pigment protein alpha chain
x: Antenna pigment protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,662102
Polymers298,26633
Non-polymers52,39669
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antenna pigment protein ... , 2 types, 28 molecules 02468bdfhjlnpx13579acegikmow

#1: Protein/peptide
Antenna pigment protein beta chain


Mass: 5044.715 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ14
#2: Protein
Antenna pigment protein alpha chain


Mass: 5993.136 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ15

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Protein , 2 types, 2 molecules AC

#3: Protein Protein LRC


Mass: 7963.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LIU2
#4: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 39580.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ18

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Reaction center protein ... , 3 types, 3 molecules HLM

#5: Protein Reaction center protein H chain


Mass: 28621.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ33
#6: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30533.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ16
#7: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 37037.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ17

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Non-polymers , 6 types, 69 molecules

#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical...
ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategoryImage processing-ID
1cryoSPARCparticle selection1
13cryoSPARC3D reconstruction1
14cryoSPARCparticle selection2
19cryoSPARC3D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.75FSC 0.143 CUT-OFF4458919LTVPOINT
22.75FSC 0.143 CUT-OFF4458919LTVPOINT
32.75FSC 0.143 CUT-OFF4458919LTVPOINT
42.75FSC 0.143 CUT-OFF4458919LTVPOINT
52.75FSC 0.143 CUT-OFF4458929LTVPOINT
62.75FSC 0.143 CUT-OFF4458929LTVPOINT
72.75FSC 0.143 CUT-OFF4458929LTVPOINT
82.75FSC 0.143 CUT-OFF4458929LTVPOINT
RefinementHighest resolution: 2.75 Å

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