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- EMDB-65393: Structure of V.cholerae dGTPase H114A octamer bound to dGTP and dAMP -

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Basic information

Entry
Database: EMDB / ID: EMD-65393
TitleStructure of V.cholerae dGTPase H114A octamer bound to dGTP and dAMP
Map data
Sample
  • Complex: dGTPase octamer
    • Protein or peptide: Deoxyguanosinetriphosphate triphosphohydrolase-like protein
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
KeywordsdGTPase / octamer / HYDROLASE
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
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsShi M / Li PP / Li QJ / Gao A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Vdg octamer
Authors: Shi M
History
DepositionJul 16, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65393.png

Downloads & links

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Map

FileDownload / File: emd_65393.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.95
Minimum - Maximum-3.8366208 - 6.3295355
Average (Standard dev.)-0.00017961841 (±0.18739165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65393_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65393_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dGTPase octamer

EntireName: dGTPase octamer
Components
  • Complex: dGTPase octamer
    • Protein or peptide: Deoxyguanosinetriphosphate triphosphohydrolase-like protein
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: dGTPase octamer

SupramoleculeName: dGTPase octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: Deoxyguanosinetriphosphate triphosphohydrolase-like protein

MacromoleculeName: Deoxyguanosinetriphosphate triphosphohydrolase-like protein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.906301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYDSEVIEYA KEQENIISKL EYRVYKHDDG RSVNRQDLMR DYARVLYSSS FRRLQGKMQL LGVDASKFNR NRLTHSLEVA QIARSIAYD LELNHTVVAE TASLAHDIGN PPFGAYGEVV LNDLSLACGG YEGNAQAFRI LRTLEKKHYA YPGLNLNVRT L MAITKYFF ...String:
MYDSEVIEYA KEQENIISKL EYRVYKHDDG RSVNRQDLMR DYARVLYSSS FRRLQGKMQL LGVDASKFNR NRLTHSLEVA QIARSIAYD LELNHTVVAE TASLAHDIGN PPFGAYGEVV 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

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Macromolecule #2: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: D5M
Molecular weightTheoretical: 331.222 Da
Chemical component information

ChemComp-D5M:
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 610983
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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