[English] 日本語
Yorodumi
- PDB-9vi0: Complex structure of BoNT-like PG1 at pH 6.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vi0
TitleComplex structure of BoNT-like PG1 at pH 6.0
Components
  • HC
  • LC
KeywordsTOXIN / LC / HC / complex
Biological speciesParaclostridium ghonii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLiu, Z. / Chen, P.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2024040801020228 China
Other government2024AFB026 China
CitationJournal: Nat Commun / Year: 2026
Title: Structure and functional divergence of the non-canonical BoNT-like toxin PG1 and PG2
Authors: Yang, J. / Liu, Z. / Jiang, L. / Ye, X. / Chao, Y. / Ren, J. / Zhu, X. / Yang, S. / Guo, X. / Zeng, J. / Wu, H. / Chen, P. / Zhang, S.
History
DepositionJun 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LC
B: HC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2853
Polymers142,2202
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein LC


Mass: 45503.875 Da / Num. of mol.: 1 / Mutation: R333A, Y336A
Source method: isolated from a genetically manipulated source
Details: LC(M1 to Q392, containing the double mutations R333A, Y336A) was expressed as a fusion protein with HC via a 14aa linker (GSGSLVPRGSGSGS) at its C-terminal. Residues N219 to E236 and the C- ...Details: LC(M1 to Q392, containing the double mutations R333A, Y336A) was expressed as a fusion protein with HC via a 14aa linker (GSGSLVPRGSGSGS) at its C-terminal. Residues N219 to E236 and the C-terminal linker region are unresolved in the density map, likely due to their flexibility.
Source: (gene. exp.) Paraclostridium ghonii (bacteria) / Strain: strain NCTR 3900 / Production host: Escherichia coli (E. coli)
#2: Protein HC


Mass: 96716.031 Da / Num. of mol.: 1 / Mutation: I5C
Source method: isolated from a genetically manipulated source
Details: HC (A2 to A838, with a I5C mutant) was expressed as a fusion protein to the C-term of LC via a 14aa linker (GSGSLVPRGSGSGS). A 6x His tag and two residue (LE) were further added to the HC C- ...Details: HC (A2 to A838, with a I5C mutant) was expressed as a fusion protein to the C-term of LC via a 14aa linker (GSGSLVPRGSGSGS). A 6x His tag and two residue (LE) were further added to the HC C-term to facilitate protein purification. Residues K403 to L413, the C-term 4 residues (F835 to A838), and the His tag regions are unresolved in the density map, likely due to their flexibility.
Source: (gene. exp.) Paraclostridium ghonii (bacteria) / Strain: strain NCTR 3900 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: Complex structure of BoNT-like PG1 at pH 6.0 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.142 MDa / Experimental value: NO
Source (natural)Organism: Paraclostridium ghonii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6 / Details: 20 mM MES, pH 6.0, 100 mM NaCl.
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodispers, the LC and HC complex.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

-
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: 1600 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
Image processingDetails: Cryo-EM imaging was performed on a Titan Krios G4 electron microscope equipped with a Gatan K3 direct electron detector and a GIF BioQuantum energy filter.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169973 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059787
ELECTRON MICROSCOPYf_angle_d0.87613218
ELECTRON MICROSCOPYf_dihedral_angle_d5.1241275
ELECTRON MICROSCOPYf_chiral_restr0.0561482
ELECTRON MICROSCOPYf_plane_restr0.0071692

+
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