[English] 日本語
Yorodumi
- PDB-9jpb: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jpb
TitleCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-containing solutions
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 4
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / reaction center / bacteria
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 / CARDIOLIPIN / : / HEME C / Chem-MW9 / SPEROIDENONE / UBIQUINONE-10 / Uncharacterized protein / Antenna pigment protein beta chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEME C / Chem-MW9 / 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: 2.8 Å
AuthorsChen, J.H. / Zheng, Q. / Zhang, X. / Wang, W. / Liu, Y. / Gu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-containing solutions
Authors: Chen, J.H. / Zheng, Q. / Zhang, X. / Wang, W. / Liu, Y. / Gu, J.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)438,542139
Polymers362,85839
Non-polymers75,684100
Water00
1


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

-
Components

-
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

-
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

-
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

-
Non-polymers , 8 types, 95 molecules

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


Mass: 911.504 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical...
ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C41H70O2
#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.: 12 / 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-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#14: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tri-Heme Cytochrome-Associated RC-LH1 Complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.423 MDa / Experimental value: YES
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: 279 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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)

-
Processing

EM software
IDNameVersionCategory
4cryoSPARC4.2.1CTF correction
10cryoSPARC4.2.1initial Euler assignment
12cryoSPARC4.5.1classification
13cryoSPARC4.5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230375 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 78.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003229324
ELECTRON MICROSCOPYf_angle_d0.635340241
ELECTRON MICROSCOPYf_chiral_restr0.03624106
ELECTRON MICROSCOPYf_plane_restr0.00494481
ELECTRON MICROSCOPYf_dihedral_angle_d14.8685246

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more