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- EMDB-66223: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type... -

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Basic information

Entry
Database: EMDB / ID: EMD-66223
TitleCryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Map data
Sample
  • Complex: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
    • Protein or peptide: Type 3 secretion system ATPase
KeywordsATPase / T3SS / TRANSLOCASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsBhattacharyya B / Chakraborty B / Datta S / Patra D
Funding support India, 1 items
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, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66223.png

Downloads & links

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Map

FileDownload / File: emd_66223.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.63 Å/pix.
x 600 pix.
= 379.8 Å		0.63 Å/pix.
x 600 pix.
= 379.8 Å		0.63 Å/pix.
x 600 pix.
= 379.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.633 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.018737871 - 1.853293
Average (Standard dev.)0.0005779427 (±0.0046422794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 379.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type...

EntireName: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Components
  • Complex: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
    • Protein or peptide: Type 3 secretion system ATPase

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Supramolecule #1: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type...

SupramoleculeName: Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)

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Macromolecule #1: Type 3 secretion system ATPase

MacromoleculeName: Type 3 secretion system ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: protein-secreting ATPase
Source (natural)Organism: Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Molecular weightTheoretical: 47.576055 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VPRGSHMNLF DSCAHPSRIH GCLLEAPLHG VFIGEICLIE RDLCQPEVIA KAQVVGFKEG QTILSLIGRA QGLTREVVIR PTGQPFVFE MGEHLAGKIY NAAGEEVGVL SNATASSEPL FTTLCRVDNP PVSVNLRRPV TTPLVTGVRA IDGLLTCGQG Q RMGIFAAA ...String:
VPRGSHMNLF DSCAHPSRIH GCLLEAPLHG VFIGEICLIE RDLCQPEVIA KAQVVGFKEG QTILSLIGRA QGLTREVVIR PTGQPFVFE MGEHLAGKIY NAAGEEVGVL SNATASSEPL FTTLCRVDNP PVSVNLRRPV TTPLVTGVRA IDGLLTCGQG Q RMGIFAAA GSGKTSLMSM IMNHAVADIC VIALIGERGR EVTEFIHELQ TSPRAAQTIL VYATSDSPAV ERCNAALLAT AM AEYFRDQ GKDVLLFVDS MTRYARALRD VALAAGELPA RRGYPASVFE QLPLLLERPG ALQHGSITAF YTVLLESEEE SDP IGDEIR SIIDGHIYLS AQLAGRGHYP AIDILHSISR VFSKVTTPQH RQDAAKTRDM LGRLAQIQLY LDLGEYQRGE NTDN DHALD NRDVIEGFLQ QAMEEPGEFS TTLNQLRELA N

UniProtKB: Type 3 secretion system ATPase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPESN-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid)
100.0 mMNaClsodium chloride
5.0 mMMgCl2Magnesium chloride

Details: 20mM HEPES, 100mM NaCl, 5mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Sample preparation #2

Preparation ID2
Concentration4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPESN-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid)
100.0 mMNaClsodium chloride
5.0 mMMgCl2Magnesium chloride

Details: 20mM HEPES, 100mM NaCl, 5mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
SoftwareName: EPU
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Digitization - Dimensions - Width: 8192 pixel / #0 - Digitization - Dimensions - Height: 8192 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 7000 / #0 - Average exposure time: 3.43 sec. / #0 - Average electron dose: 40.0 e/Å2 / #0 - Details: 40 frames per movie / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Digitization - Dimensions - Width: 8192 pixel / #1 - Digitization - Dimensions - Height: 8192 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 3600 / #1 - Average exposure time: 3.43 sec. / #1 - Average electron dose: 40.0 e/Å2 / #1 - Details: 40 frames per movie
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Image recording ID1
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Software - details: Patch CTF estimation progam was used. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Insilico model was generated using Ab-initio Reconstruction program of CryoSPARC 4.6.2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 4.6.2)Non Uniform Refinement used
UCSF ChimeraX

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.
Number images used: 174701
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 150000 / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Heterogenous Refinement Program used.

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Atomic model buiding 1

Initial modelPDB ID:

7-f1


Chain - Residue range: 1-430 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.9)
Details: Alphafold model was rigid-body fit into the map using ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9wto:
Cryo-EM Structure of the 12-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica

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