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- PDB-9wto: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type... -

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Basic information

Entry
Database: PDB / ID: 9wto
TitleCryo-EM Structure of the 12-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-secreting ATPase / protein-exporting ATPase activity / 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 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Authors: Bhattacharyya, B. / Chakraborty, B. / Datta, S. / Patra, D.
History
DepositionSep 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
L: Type 3 secretion system ATPase


Theoretical massNumber of molelcules
Total (without water)570,91312
Polymers570,91312
Non-polymers00
Water00
1


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

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Components

#1: Protein
Type 3 secretion system ATPase


Mass: 47576.055 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Gene: ysaN, YE3544 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1JQ97, protein-secreting ATPase
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cryo-EM Structure of the 12-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
Vitrification
IDInstrumentCryogen nameHumidity (%)Specimen-IDChamber temperature (K)Entry-ID
1FEI VITROBOT MARK IVETHANE9512899WTO
2FEI VITROBOT MARK IVETHANE9522899WTO

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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
81928192119WTO
81928192229WTO

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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.
10PHENIX1.21.2_5419:model refinementphenix.real_space_refine was used for final refinement.
11cryoSPARC4.6.2initial Euler assignment
12cryoSPARC4.6.2final Euler assignment
13cryoSPARC4.6.2classificationHeterogenous Refinement Program used.
14cryoSPARC4.6.23D reconstructionNon Uniform Refinement used
15UCSF ChimeraX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174701
Details: The composite map was generated using a consensus map and a focus map in ChimeraX using volume maximum command. The reported resolution corresponding to the gold-standard FSC (0.143) of the ...Details: The composite map was generated using a consensus map and a focus map in ChimeraX using volume maximum command. The reported resolution corresponding to the gold-standard FSC (0.143) of the consensus 11-mer reconstruction, which constitutes majority of the map.
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_d0.00238046
ELECTRON MICROSCOPYf_angle_d0.57651764
ELECTRON MICROSCOPYf_dihedral_angle_d3.8415433
ELECTRON MICROSCOPYf_chiral_restr0.0426170
ELECTRON MICROSCOPYf_plane_restr0.0036829

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