[English] 日本語
Yorodumi
- PDB-9kzh: Cryo-EM structure of the RC complex from Rhodospirillum rubrum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kzh
TitleCryo-EM structure of the RC complex from Rhodospirillum rubrum
Components
  • (Reaction center protein ...) x 2
  • Photoreaction center protein H
KeywordsSTRUCTURAL PROTEIN / light harvesting / photosynthesis / gene heterologous expression / Rhodospirillum rubrum
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / metal ion binding
Similarity search - Function
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 / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily ...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 / Photosynthetic reaction centre, L subunit / PRC-barrel-like 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
Trans-Geranyl BACTERIOCHLOROPHYLL A / Trans-Geranyl BACTERIOPHEOPHYTIN A / Octadecane / CARDIOLIPIN / SPIRILLOXANTHIN / : / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / Chem-RQ0 / UBIQUINONE-10 ...Trans-Geranyl BACTERIOCHLOROPHYLL A / Trans-Geranyl BACTERIOPHEOPHYTIN A / Octadecane / CARDIOLIPIN / SPIRILLOXANTHIN / : / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / Chem-RQ0 / UBIQUINONE-10 / Reaction center protein L chain / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang, L. / Yu, L.-J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC341800 China
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Assembly, selectivity, and compatibility of bacterial photosynthetic complexes from divergent species detected in a chimeric strain.
Authors: Lu Wang / Yi-Hao Yan / Guang-Lei Wang / Xing-Yu Yue / Chen-Hui Qi / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Yueyong Xin / Long-Jiang Yu /
Abstract: Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein ...Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein structures is a topic of great interest, and assembly mechanisms appear to reflect the evolutionary diversity of the particular phototrophic organism. Here we constructed a photosynthetic chimera expressing the Roseiflexus castenholzii LH and Rhodospirillum rubrum RC complexes in a photocomplex-deficient Rsp. rubrum mutant, and spectroscopy confirmed LH expression with absorption maxima at 878 and 801 nm. The chimeric strain grew slower phototrophically than wildtype but faster than a strain containing only the RC, indicating partial energy transfer from LH to RC. Cryo-EM structural analysis revealed that the Rfl. castenholzii LH independently assembled into a closed ring of 15 αβ heterodimers lacking carotenoids, resulting in a blue-shifted Q transition, while the Rsp. rubrum RC formed a separate complex with an RC:LH ratio of ∼17:1 instead of a typical 1:1. Structural differences, including the absence of two Rfl. castenholzii-specific small proteins, likely precluded formation of a conjoined LH-RC in the chimeric strain. These results reveal that distinct photocomplex assembly strategies exist in phylogenetically divergent species and underscore the modularity and adaptability of photosynthetic complexes, offering insights for artificial photosystem design.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data 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
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Photoreaction center protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,65548
Polymers92,8713
Non-polymers30,78445
Water00
1


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

-
Components

-
Reaction center protein ... , 2 types, 2 molecules LM

#1: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30660.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: P10717
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34234.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: P10718

-
Protein / Sugars , 2 types, 2 molecules H

#3: Protein Photoreaction center protein H / Reaction center protein H chain


Mass: 27976.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: Q7M149
#8: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 10 types, 44 molecules

#4: Chemical
ChemComp-07D / Trans-Geranyl BACTERIOCHLOROPHYLL A


Mass: 901.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H64MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-08I / Trans-Geranyl BACTERIOPHEOPHYTIN A


Mass: 879.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H66N4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#9: Chemical
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H38
#10: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#11: 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
#12: Chemical ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-RQ0 / 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione


Mass: 844.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H85NO3 / Feature type: SUBJECT OF INVESTIGATION
#14: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RC COMPLEX / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Source (recombinant)Organism: Rhodospirillum rubrum (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 60.24 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118603 / Symmetry type: POINT
RefinementHighest resolution: 2.74 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058542
ELECTRON MICROSCOPYf_angle_d0.83411438
ELECTRON MICROSCOPYf_dihedral_angle_d19.4753593
ELECTRON MICROSCOPYf_chiral_restr0.0461109
ELECTRON MICROSCOPYf_plane_restr0.0051309

+
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