[English] 日本語
Yorodumi
- EMDB-66287: CryoEM structure of a dNTPase from Vibrio cholerae with GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66287
TitleCryoEM structure of a dNTPase from Vibrio cholerae with GTP
Map data
Sample
  • Complex: dNTPase
    • Protein or peptide: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsdNTPase / Vibrio cholerae / defense / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process
Similarity search - Function
dNTP triphosphohydrolase, type 2 / Phosphohydrolase-associated domain / Phosphohydrolase-associated domain / dNTP triphosphohydrolase / : / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsXu ZX / Zhang K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of a dNTPase from Vibrio cholerae
Authors: Xu ZX / Zhang K
History
DepositionSep 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66287.png

Downloads & links

-
Map

FileDownload / File: emd_66287.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 360 pix.
= 307.8 Å		0.86 Å/pix.
x 360 pix.
= 307.8 Å		0.86 Å/pix.
x 360 pix.
= 307.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-16.945105000000002 - 33.627290000000002
Average (Standard dev.)0.000000000000467 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 307.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66287_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66287_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : dNTPase

EntireName: dNTPase
Components
  • Complex: dNTPase
    • Protein or peptide: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water

-
Supramolecule #1: dNTPase

SupramoleculeName: dNTPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)

-
Macromolecule #1: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2

MacromoleculeName: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Molecular weightTheoretical: 45.973367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYDSEVIEYA KEQENIISKL EYRVYKHDDG RSVNRQDLMR DYARVLYSSS FRRLQGKMQL LGVDASKFNR NRLTHSLEVA QIARSIAYD LELNHTVVAE TASLAHDIGN PPFGHYGEVV LNDLSLACGG YEGNAQAFRI LRTLEKKHYA YPGLNLNVRT L MAITKYFF ...String:
MYDSEVIEYA KEQENIISKL EYRVYKHDDG RSVNRQDLMR DYARVLYSSS FRRLQGKMQL LGVDASKFNR NRLTHSLEVA QIARSIAYD LELNHTVVAE TASLAHDIGN PPFGHYGEVV LNDLSLACGG YEGNAQAFRI LRTLEKKHYA YPGLNLNVRT L MAITKYFF NKHQNNKKFL YDADYEFLKT ELDSKGVTVT KSIDAEIMDL ADEIAYAAHD LEDALSFGMI SLGEIVHEFS IS DKFKDAY PTMTDIAKEA QNVAMKASRS GTSEEYAIVL KKELTSMIVN ILCSDIGLVD GCLGYKRHAK LAEGLKKLLF KAI LRKKDI QLYERRGEQI IRGLFEVYSD EKYNKDNMLL PPELRAINDC KTRLVTDYIS GMMDSYAAQE YEKYFGKGSA DKLY FK

UniProtKB: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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