[English] 日本語
Yorodumi
- PDB-9wqv: Cryo-EM structure of LH1-RC from Rhodovulum sulfidophilum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wqv
TitleCryo-EM structure of LH1-RC from Rhodovulum sulfidophilum
Components
  • (Antenna pigment protein ...) x 2
  • (Reaction center protein ...) x 2
  • NADH:ubiquinone oxidoreductase 41 kd complex i subunit
  • Photosynthetic reaction center cytochrome c subunit
  • photosynthetic reaction center subunit H
KeywordsPHOTOSYNTHESIS / light harvesting complex 1 / Rhodovulum sulfidophilum
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, M subunit / 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 / : / HEME C / Chem-PGV / SPHEROIDENE / UBIQUINONE-10 / Unknown ligand / Antenna pigment protein beta chain ...: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / HEME C / Chem-PGV / SPHEROIDENE / UBIQUINONE-10 / Unknown ligand / 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
Similarity search - Component
Biological speciesRhodovulum sulfidophilum DSM 1374 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.81 Å
AuthorsYue, X.-Y. / Wang, G.-L. / Yu, L.-J.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)ZR2019ZD48 China
Ministry of Science and Technology (MoST, China)2022SZX12 China
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into the photochemistry of the LH1-RC complex from the marine purple phototrophic bacterium Rhodovulum sulfidophilum.
Authors: Xing-Yu Yue / Guang-Lei Wang / Shinya Kosaki / Kenji V P Nagashima / Yu-Lu Wu / Yuki Kobayashi / Tomoya Sugiyama / Ryo Kanno / Endang R Purba / Shinichi Takaichi / Toshiaki Mochizuki / Akira ...Authors: Xing-Yu Yue / Guang-Lei Wang / Shinya Kosaki / Kenji V P Nagashima / Yu-Lu Wu / Yuki Kobayashi / Tomoya Sugiyama / Ryo Kanno / Endang R Purba / Shinichi Takaichi / Toshiaki Mochizuki / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Hiroyuki Mino / Kazutoshi Tani / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Long-Jiang Yu /
Abstract: The marine purple nonsulfur phototrophic bacterium Rhodovulum (Rdv.) sulfidophilum (Alphaproteobacteria) has been a model organism for bacterial photosynthesis research because of its unusual ability ...The marine purple nonsulfur phototrophic bacterium Rhodovulum (Rdv.) sulfidophilum (Alphaproteobacteria) has been a model organism for bacterial photosynthesis research because of its unusual ability to grow phototrophically (anoxic/light) using high concentrations of inorganic or organic sulfur compounds as electron donors or by respiration under fully oxic conditions. Here we present a 1.81 Å-resolution cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) photocomplex from the Rdv. sulfidophilum type strain W4 with a focus on RC structure and function. The Rdv. sulfidophilum RC is characterized by its cytochrome (Cyt) subunit that contains three heme groups and is anchored by its intact N-terminal domain in the membrane. In contrast to a methionine as the 6th axial ligand to the heme-2 in other bacterial RC-bound triheme and tetraheme Cyt subunits, the outmost heme-2 in the Rdv. sulfidophilum Cyt subunit is ligated by a cysteine residue, resulting in a significant downshift of reduction potential of 470 mV compared to that of a methionine-ligated heme-2. A nonheme Fe ligated by a histidine of the Cyt subunit and five water molecules was identified in close proximity to heme-2, implying a potential role in electron transport from soluble electron donors to heme-2. The Rdv. sulfidophilum LH1 complex forms an open ring structure consisting of 16 αβ-subunits with a gap formed where the N-terminal transmembrane domain of the RC Cyt subunit and a newly identified protein with three helical domains (designated as protein-3h) are located. Protein-3h corresponds to the truncated N-terminal fragment of a gene product encoded by the pseudo-gene urf1 in the NADH:ubiquinone oxidoreductase (complex I) nuo operon in the genome of Rdv. sulfidophilum W4. Genes urf1 are also found in other purple nonsulfur bacteria and in aerobic anoxygenic phototrophic bacteria, and their putative products all share a common structural motif of N-terminal transmembrane U-shaped tandem helices. Based on structural and spectroscopic data, possible electron transfer pathways between the Rdv. sulfidophilum RC Cyt subunit and soluble electron donors and potential roles of protein-3h in the structural integrity of LH1-RC are discussed.
History
DepositionSep 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 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
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: Antenna pigment protein alpha chain
B: Antenna pigment protein beta chain
C: Photosynthetic reaction center cytochrome c subunit
D: Antenna pigment protein alpha chain
E: Antenna pigment protein beta chain
F: Antenna pigment protein alpha chain
G: Antenna pigment protein beta chain
H: photosynthetic reaction center subunit H
I: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
K: Antenna pigment protein alpha chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Antenna pigment protein beta chain
O: Antenna pigment protein alpha chain
P: Antenna pigment protein beta chain
Q: Antenna pigment protein alpha chain
R: Antenna pigment protein beta chain
S: Antenna pigment protein alpha chain
T: Antenna pigment protein beta chain
U: Antenna pigment protein alpha chain
V: Antenna pigment protein beta chain
W: Antenna pigment protein alpha chain
X: Antenna pigment protein beta chain
Y: Antenna pigment protein alpha chain
Z: Antenna pigment protein beta chain
a: NADH:ubiquinone oxidoreductase 41 kd complex i subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,987154
Polymers346,85437
Non-polymers75,133117
Water9,044502
1


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

-
Components

-
Antenna pigment protein ... , 2 types, 32 molecules 02468BEGJNPRTVXZ13579ADFIKOQSUWY

#1: Protein/peptide
Antenna pigment protein beta chain


Mass: 5427.191 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXD9 temporarily.
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
References: UniProt: Q9WXD9
#2: Protein
Antenna pigment protein alpha chain


Mass: 6238.516 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE0 temporarily.
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
References: UniProt: Q9WXE0

-
Protein , 3 types, 3 molecules CHa

#3: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 39176.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
References: UniProt: Q9WXE3
#4: Protein photosynthetic reaction center subunit H


Mass: 28762.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
#7: Protein NADH:ubiquinone oxidoreductase 41 kd complex i subunit


Mass: 24079.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)

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

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


Mass: 31674.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE1 temporarily.
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
References: UniProt: Q9WXE1
#6: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 36508.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The sequence of organism Rhodovulum sulfidophilum DSM 1374 is not available during the biocuration, replaced by Q9WXE2 temporarily.
Source: (natural) Rhodovulum sulfidophilum DSM 1374 (bacteria)
References: UniProt: Q9WXE2

-
Sugars , 1 types, 10 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 11 types, 609 molecules

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


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 254.494 Da / Num. of mol.: 13 / Source method: obtained synthetically
#10: Chemical
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C41H60O / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-A1EYK / (4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol / Demethylspheroidene


Mass: 554.888 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H58O / Feature type: SUBJECT OF INVESTIGATION
#13: 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.: 13 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#14: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#17: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
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: LH1-RC / Type: COMPLEX / Entity ID: #3, #5-#6, #4, #2, #1, #7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodovulum sulfidophilum DSM 1374 (bacteria)
Buffer solutionpH: 8
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: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 1.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108964 / Symmetry type: POINT

+
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