[English] 日本語
Yorodumi
- PDB-9wd4: Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wd4
TitleCryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
ComponentsType 3 secretion system ATPase
KeywordsTRANSLOCASE / ATPase / T3SS
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / : / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 3 secretion system ATPase
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsBhattacharyya, B. / Chakraborty, B. / Datta, S. / Patra, D.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)RDS000002 India
CitationJournal: To Be Published
Title: Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Authors: Bhattacharyya, B. / Chakraborty, B. / Datta, S. / Patra, D.
History
DepositionAug 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 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
A: Type 3 secretion system ATPase
B: Type 3 secretion system ATPase
C: Type 3 secretion system ATPase
D: Type 3 secretion system ATPase
E: Type 3 secretion system ATPase
F: Type 3 secretion system ATPase
G: Type 3 secretion system ATPase
H: Type 3 secretion system ATPase
I: Type 3 secretion system ATPase
J: Type 3 secretion system ATPase
K: Type 3 secretion system ATPase


Theoretical massNumber of molelcules
Total (without water)523,33711
Polymers523,33711
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 3 secretion system ATPase


Mass: 47576.055 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Details: YsaN homo 11-mer
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Strain: NCTC 13174 / 8081 (8081) / Gene: ysaN, YE3544 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / BL21-DE3 / References: UniProt: A1JQ97, protein-secreting ATPase
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solution
IDSpecimen-IDpHDetails (eV)
117.420mM HEPES, 100mM NaCl, 5mM MgCl2
227.420mM Tris-HCl, 100mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMN-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid)HEPES1
2100 mMsodium chlorideNaCl1
35 mMMagnesium chlorideMgCl21
420 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl2
5100 mMsodium chlorideNaCl2
Specimen
IDConc. (mg/ml)Experiment-IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
131NONONOYES
241NONONOYES
Specimen support
IDSpecimen-IDDetails (eV)Grid materialGrid mesh size (divisions/in.)Grid type
11The grid was glow-discharged at 15 mA for 60 s under 0.39 mBar pressure.GOLD300UltrAuFoil R1.2/1.3
22The grid was glow-discharged at 15 mA for 30 s under 0.39 mBar pressure.COPPER300Quantifoil R1.2/1.3
Vitrification
IDInstrumentCryogen nameHumidity (%)Specimen-IDChamber temperature (K)Entry-ID
1FEI VITROBOT MARK IVETHANE9512899WD4
2FEI VITROBOT MARK IVETHANE9522899WD4

-
Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recording

Imaging-ID: 1 / Average exposure time: 3.43 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Details: 40 frames per movie

IDNum. of real images
17000
23600
Image scans
WidthHeightIDImage recording-IDEntry-ID
81928192119WD4
81928192229WD4

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6.2particle selectionParticles are initially picked with blob picker to generate 2D template. Final set of particles are picked with template picker.
2EPUimage acquisition
4cryoSPARC4.6.2CTF correctionPatch CTF estimation progam was used.
7UCSF ChimeraX1.9model fittingAlphafold model was rigid-body fit into the map using ChimeraX
8Coot0.9.8.95model fittingUsed to manual refinement.
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classificationHeterogenous Refinement Program used.
13cryoSPARC4.6.23D reconstructionNon Uniform Refinement used
14PHENIX1.21.2_5419:model refinementphenix.real_space_refine was used for final refinement.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174701 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingAccession code: AF-A1JQ97-F1 / Chain residue range: 1-430 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00433230
ELECTRON MICROSCOPYf_angle_d0.51645156
ELECTRON MICROSCOPYf_dihedral_angle_d4.2584761
ELECTRON MICROSCOPYf_chiral_restr0.0425365
ELECTRON MICROSCOPYf_plane_restr0.0035935

+
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