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- PDB-9km0: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 comp... -

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Basic information

Entry
Database: PDB / ID: 9km0
TitleCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na-containing solutions
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 4
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / Reaction center / energy transfer
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 / 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 / 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 / CARDIOLIPIN / : / HEME C / Chem-MW9 / UBIQUINONE-10 / Uncharacterized protein / Antenna pigment protein beta chain ...: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEME C / Chem-MW9 / 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: 2.78 Å
AuthorsChen, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Cryo-EM Analysis of a Tri-Heme Cytochrome-Associated RC-LH1 Complex from the Marine Photoheterotrophic Bacterium Dinoroseobacter Shibae.
Authors: Weiwei Wang / Yanting Liu / Jiayi Gu / Shaoya An / Cheng Ma / Haichun Gao / Nianzhi Jiao / Jian-Ren Shen / John Thomas Beatty / Michal Koblížek / Xing Zhang / Qiang Zheng / Jing-Hua Chen /
Abstract: The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy ...The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy structure of the RC-LH1 isolated from a marine photoheterotrophic bacterium Dinoroseobacter shibae. The RC comprises four subunits, including a three-heme cytochrome (Cyt) c protein, and is surrounded by a closed LH ring composed of 17 pairs of antenna subunits. Notably, a novel subunit with an N-terminal "helix-turn-helix" motif embedded in the gap between the RC and the LH ring is identified. The purified RC-LH1 complex exhibits high stability in solutions containing Mg or Ca. The periplasmic Cyt c is predicted to bind at the junction between the Cyt subunit and the membrane plane, enabling electron transfer from Cyt c to the proximal heme of the tri-heme Cyt, and subsequently to the special pair of bacteriochlorophylls. These findings provide structural insights into the efficient energy and electron transfer processes within a distinct type of RC-LH1, and shed light on evolutionary adaptations of photosynthesis.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Antenna pigment protein alpha chain
O: Reaction center protein O chain
V: Antenna pigment protein alpha chain
v: Antenna pigment protein beta chain
S: Antenna pigment protein alpha chain
t: Antenna pigment protein beta chain
T: Antenna pigment protein alpha chain
s: Antenna pigment protein beta chain
Q: Antenna pigment protein alpha chain
r: Antenna pigment protein beta chain
R: Antenna pigment protein alpha chain
q: Antenna pigment protein beta chain
p: Antenna pigment protein beta chain
2: Antenna pigment protein beta chain
1: Antenna pigment protein alpha chain
n: Antenna pigment protein beta chain
N: Antenna pigment protein alpha chain
k: Antenna pigment protein beta chain
K: Antenna pigment protein alpha chain
j: Antenna pigment protein beta chain
J: Antenna pigment protein alpha chain
i: Antenna pigment protein beta chain
I: Antenna pigment protein alpha chain
g: Antenna pigment protein beta chain
G: Antenna pigment protein alpha chain
f: Antenna pigment protein beta chain
F: Antenna pigment protein alpha chain
e: Antenna pigment protein beta chain
E: Antenna pigment protein alpha chain
d: Antenna pigment protein beta chain
D: Antenna pigment protein alpha chain
b: Antenna pigment protein beta chain
B: Antenna pigment protein alpha chain
a: Antenna pigment protein beta chain
A: Antenna pigment protein alpha chain
M: Reaction center protein M chain
L: Reaction center protein L chain
H: Reaction center protein H chain
C: Photosynthetic reaction center cytochrome c subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,565137
Polymers362,85839
Non-polymers73,70798
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, 34 molecules PVSTQR1NKJIGFEDBAvtsrqp2nkjigf...

#1: Protein
Antenna pigment protein alpha chain / Light-harvesting antenna LH1 / alpha subunit


Mass: 6195.409 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ15
#3: Protein/peptide
Antenna pigment protein beta chain / Light-harvesting antenna LH1 / beta subunit


Mass: 5578.334 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ14

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Reaction center protein ... , 4 types, 4 molecules OMLH

#2: Protein Reaction center protein O chain


Mass: 25206.586 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 Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 37583.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ17
#5: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31197.178 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 H chain / Photosynthetic reaction center subunit H


Mass: 28739.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
References: UniProt: A8LQ33

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Protein / Sugars , 2 types, 6 molecules C

#11: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#7: Protein Photosynthetic reaction center cytochrome c subunit / PufC


Mass: 39977.367 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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Non-polymers , 8 types, 93 molecules

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


Mass: 911.504 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#9: Chemical...
ChemComp-A1EFU / (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one / Spheroidenone


Mass: 582.898 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C41H58O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
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 / 1-stearoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)


Mass: 777.060 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C42H81O10P
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: 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
#14: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#15: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / 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: tri-heme cytochrome-associated RC-LH1 complex / 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4.5.1CTF correction
10cryoSPARC4.5.1initial Euler assignment
11cryoSPARC4.5.1final Euler assignment
12cryoSPARC4.5.1classification
13cryoSPARC4.5.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230375 / Num. of class averages: 10 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003229320
ELECTRON MICROSCOPYf_angle_d0.615940243
ELECTRON MICROSCOPYf_chiral_restr0.03533928
ELECTRON MICROSCOPYf_plane_restr0.0054525
ELECTRON MICROSCOPYf_dihedral_angle_d15.3495671

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