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- EMDB-60843: GNATD focused acetyltransferase -

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Basic information

Entry
Database: EMDB / ID: EMD-60843
TitleGNATD focused acetyltransferase
Map data
Sample
  • Complex: Acetyltransferase
KeywordsAcetyltransferase / TRANSFERASE
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsPark JB / Rho SH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ.
Authors: Park JB / Lee G / Han YY / Kim D / Heo K / Kim J / Park J / Yun H / Lee CW / Cho HS / Kim JS / Steinegger M / Seok YJ / Roh SH
#1: Journal: mBio / Year: 2018
Title: Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli.
Authors: Christensen DG / Meyer JG / Baumgartner JT / D'Souza AK / Nelson WC / Payne SH / Kuhn ML / Schilling B / Wolfe AJ
History
DepositionJul 18, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_60843.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.723 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-1.2556884 - 2.0079548
Average (Standard dev.)0.0001285079 (±0.00666063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 323.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Acetyltransferase

EntireName: Acetyltransferase
Components
  • Complex: Acetyltransferase

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Supramolecule #1: Acetyltransferase

SupramoleculeName: Acetyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2195848
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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