[English] 日本語
Yorodumi
- PDB-9wfd: Cryo-EM structure of the Type II secretion system protein from Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wfd
TitleCryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
ComponentsType II and III secretion system protein
KeywordsTOXIN / --Type II secretion system protein / Acidithiobacillus caldus
Function / homologyPilus formation protein, N-terminal / Pilus formation protein N terminal region / GspD/PilQ family / : / Type II/III secretion system / Bacterial type II and III secretion system protein / type II protein secretion system complex / protein secretion / Type II and III secretion system protein
Function and homology information
Biological speciesAcidithiobacillus caldus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsLiu, R.H. / Zhang, K. / Feng, Q.S. / Dai, X. / Zhang, X. / Li, W. / Bao, Z.P. / Lin, W.F. / Fu, Y. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Funct Mater / Year: 2025
Title: Unveiling Acidophilic Secretin Nanopores for Ion Exclusion and Single-Molecule Sensing
Authors: Liu, R. / Zhang, K. / Feng, Q. / He, S. / Fan, Q. / Zhang, X. / Li, W. / Bao, Z. / Lin, W. / Fu, Y. / Li, Y.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type II and III secretion system protein
B: Type II and III secretion system protein
C: Type II and III secretion system protein
D: Type II and III secretion system protein
E: Type II and III secretion system protein
F: Type II and III secretion system protein
G: Type II and III secretion system protein
H: Type II and III secretion system protein
I: Type II and III secretion system protein
J: Type II and III secretion system protein
K: Type II and III secretion system protein
L: Type II and III secretion system protein
M: Type II and III secretion system protein
N: Type II and III secretion system protein


Theoretical massNumber of molelcules
Total (without water)749,78714
Polymers749,78714
Non-polymers00
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
Type II and III secretion system protein


Mass: 53556.238 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus caldus (strain SM-1) (bacteria)
Gene: Atc_2749 / Production host: Escherichia coli (E. coli) / References: UniProt: F9ZTP9
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Type II secretion system protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acidithiobacillus caldus (strain SM-1) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: 3200 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 452989
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72834 / Symmetry type: POINT
RefinementHighest resolution: 2.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00846060
ELECTRON MICROSCOPYf_angle_d0.75562692
ELECTRON MICROSCOPYf_dihedral_angle_d5.7836412
ELECTRON MICROSCOPYf_chiral_restr0.0517518
ELECTRON MICROSCOPYf_plane_restr0.0078176

+
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