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- EMDB-65920: Cryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type... -

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Basic information

Entry
Database: EMDB / ID: EMD-65920
TitleCryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Map data
Sample
  • Complex: Cryo-EM Structure of the 13-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-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 13-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Authors: Bhattacharyya B / Chakraborty B / Datta S / Patra D
History
DepositionAug 20, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65920.png

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Map

FileDownload / File: emd_65920.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.633 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.1582095 - 0.22837256
Average (Standard dev.)-0.00003939575 (±0.005607692)
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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Additional map: #1

Fileemd_65920_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65920_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65920_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type...

EntireName: Cryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Components
  • Complex: Cryo-EM Structure of the 13-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 13-Mer ATPase Complex YsaN from the Type...

SupramoleculeName: Cryo-EM Structure of the 13-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: 13 / Enantiomer: LEVO / EC number: protein-secreting ATPase
Source (natural)Organism: Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Molecular weightTheoretical: 46.94034 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNLFDSCAHP SRIHGCLLEA PLHGVFIGEI CLIERDLCQP EVIAKAQVVG FKEGQTILSL IGRAQGLTRE VVIRPTGQPF VFEMGEHLA GKIYNAAGEE VGVLSNATAS SEPLFTTLCR VDNPPVSVNL RRPVTTPLVT GVRAIDGLLT CGQGQRMGIF A AAGSGKTS ...String:
MNLFDSCAHP SRIHGCLLEA PLHGVFIGEI CLIERDLCQP EVIAKAQVVG FKEGQTILSL IGRAQGLTRE VVIRPTGQPF VFEMGEHLA GKIYNAAGEE VGVLSNATAS SEPLFTTLCR VDNPPVSVNL RRPVTTPLVT GVRAIDGLLT CGQGQRMGIF A AAGSGKTS LMSMIMNHAV ADICVIALIG ERGREVTEFI HELQTSPRAA QTILVYATSD SPAVERCNAA LLATAMAEYF RD QGKDVLL FVDSMTRYAR ALRDVALAAG ELPARRGYPA SVFEQLPLLL ERPGALQHGS ITAFYTVLLE SEEESDPIGD EIR SIIDGH IYLSAQLAGR GHYPAIDILH SISRVFSKVT TPQHRQDAAK TRDMLGRLAQ IQLYLDLGEY QRGENTDNDH ALDN RDVIE GFLQQAMEEP GEFSTTLNQL RELAN

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 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
100.0 mMNaClsodium chloride

Details: 20mM Tris-HCl, 100mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: The grid was glow-discharged at 15mA for 60 s under 0.39 mBar pressure.
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 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
100.0 mMNaClsodium chloride

Details: 20mM Tris-HCl, 100mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: The grid was glow-discharged at 15mA for 60 s under 0.39 mBar pressure.
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Non Uniform Refinement used / Number images used: 123350
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.
FSC plot (resolution estimation)

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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-9wf0:
Cryo-EM Structure of the 13-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica

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