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

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Basic information

Entry
Database: PDB / ID: 9ltu
TitleCryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 1)
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
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 ...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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / SPEROIDENONE / UBIQUINONE-10 / Antenna pigment protein beta chain / Antenna pigment protein alpha chain / Reaction center protein L chain / Reaction center protein M chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / SPEROIDENONE / UBIQUINONE-10 / 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: 2.44 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: To Be Published
Title: Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 1)
Authors: Liu, Z.K. / Wang, P. / Liu, L.N.
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

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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
7: Antenna pigment protein alpha chain
8: Antenna pigment protein beta chain
9: Antenna pigment protein alpha chain
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,22777
Polymers246,15124
Non-polymers40,07653
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, 20 molecules 08bdfhjlnp79acegikmo

#1: Protein/peptide
Antenna pigment protein beta chain


Mass: 5044.715 Da / Num. of mol.: 10 / 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.: 10 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ15

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Protein , 1 types, 1 molecules C

#3: 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

#4: 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
#5: 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
#6: 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, 53 molecules

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


Mass: 911.504 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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 1)
Type: COMPLEX / Entity ID: #1-#6 / 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 selection3
19cryoSPARC3D reconstruction3
Image processing
IDImage recording-ID
11
21
31
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.44FSC 0.143 CUT-OFF8283019LTUPOINT
22.44FSC 0.143 CUT-OFF8283019LTUPOINT
32.44FSC 0.143 CUT-OFF8283019LTUPOINT
42.44FSC 0.143 CUT-OFF8283029LTUPOINT
52.44FSC 0.143 CUT-OFF8283029LTUPOINT
62.44FSC 0.143 CUT-OFF8283029LTUPOINT
72.44FSC 0.143 CUT-OFF8283039LTUPOINT
82.44FSC 0.143 CUT-OFF8283039LTUPOINT
92.44FSC 0.143 CUT-OFF8283039LTUPOINT
RefinementHighest resolution: 2.44 Å

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