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- EMDB-52126: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexame... -

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Basic information

Entry
Database: EMDB / ID: EMD-52126
TitleCryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with 5mdCTP bound in the active site
Map data
Sample
  • Complex: Human CDADC1 hexamer with bound 5mdCTP
    • Protein or peptide: Cytidine and dCMP deaminase domain-containing protein 1
  • Ligand: ZINC ION
  • Ligand: [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: water
KeywordsHuman dCTP deaminase / trimer / Zinc-dependent / Nucleotide metabolism / HYDROLASE
Function / homology
Function and homology information


dCMP deaminase activity / cytidine deaminase / importin-alpha family protein binding / : / DNA cytosine deamination / cytidine deaminase activity / protein homodimerization activity / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Deoxycytidylate deaminase domain / Deoxycytidylate deaminase-related / Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
Cytidine and dCMP deaminase domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSlyvka A / Rathore I / Yang R / Kanai T / Lountos G / Wang Z / Skowronek K / Czarnocki-Cieciura M / Wlodawer A / Bochtler M
Funding support Poland, United States, 4 items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-5D81/17-00 Poland
Ministry of Science and Higher Education (Poland)PPI/APM/2018/1/00034 Poland
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH Intramural Research Program United States
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: To Be Published / Year: 2025
Title: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer without a ligand
Authors: Slyvka A / Rathore I / Yang R / Kanai T / Lountos G / Wang Z / Skowronek K / Czarnocki-Cieciura M / Wlodawer A / Bochtler M
History
DepositionNov 18, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52126.png

Downloads & links

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Map

FileDownload / File: emd_52126.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.4860466 - 2.2868202
Average (Standard dev.)-0.0012005792 (±0.094145834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52126_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52126_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 : Human CDADC1 hexamer with bound 5mdCTP

EntireName: Human CDADC1 hexamer with bound 5mdCTP
Components
  • Complex: Human CDADC1 hexamer with bound 5mdCTP
    • Protein or peptide: Cytidine and dCMP deaminase domain-containing protein 1
  • Ligand: ZINC ION
  • Ligand: [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: water

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Supramolecule #1: Human CDADC1 hexamer with bound 5mdCTP

SupramoleculeName: Human CDADC1 hexamer with bound 5mdCTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 363 KDa

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Macromolecule #1: Cytidine and dCMP deaminase domain-containing protein 1

MacromoleculeName: Cytidine and dCMP deaminase domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: cytidine deaminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.65232 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKEAGQMQNL ESARAGRSVS TQTGSMTGQI PRLSKVNLFT LLSLWMELFP AEAQRQKSQK NEEGKHGPL GDNEERTRVS TDKRQVKRTG LVVVKNMKIV GLHCSSEDLH AGQIALIKHG SRLKNCDLYF SRKPCSACLK M IVNAGVNR ...String:
MGSSHHHHHH SSGLVPRGSH MKEAGQMQNL ESARAGRSVS TQTGSMTGQI PRLSKVNLFT LLSLWMELFP AEAQRQKSQK NEEGKHGPL GDNEERTRVS TDKRQVKRTG LVVVKNMKIV GLHCSSEDLH AGQIALIKHG SRLKNCDLYF SRKPCSACLK M IVNAGVNR ISYWPADPEI SLLTEASSSE DAKLDAKAVE RLKSNSRAHV CVLLQPLVCY MVQFVEETSY KCDFIQKITK TL PDANTDF YYECKQERIK EYEMLFLVSN EEMHKQILMT IGLENLCENP YFSNLRQNMK DLILLLATVA SSVPNFKHFG FYR SNPEQI NEIHNQSLPQ EIARHCMVQA RLLAYRTEDH KTGVGAVIWA EGKSRSCDGT GAMYFVGCGY NAFPVGSEYA DFPH MDDKQ KDREIRKFRY IIHAAQNALT FRCQEIKPEE RSMIFVTKCP CDECVPLIKG AGIKQIYAGD VDVGKKKADI SYMRF GELE GVSKFTWQLN PSGAYGLEQN EPERRENGVL RPVPQKEEQH QDKKLRLGIH

UniProtKB: Cytidine and dCMP deaminase domain-containing protein 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimi...

MacromoleculeName: [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
type: ligand / ID: 3 / Number of copies: 6 / Formula: A1I2I
Molecular weightTheoretical: 481.184 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 112912
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9hft:
Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with 5mdCTP bound in the active site

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