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- PDB-9hfs: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexame... -

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Basic information

Entry
Database: PDB / ID: 9hfs
TitleCryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with dCTP bound in the active site
ComponentsCytidine and dCMP deaminase domain-containing protein 1
KeywordsHYDROLASE / Human dCTP deaminase / trimer / Zinc-dependent / Nucleotide metabolism
Function / homology
Function and homology information


dCMP deaminase activity / cytidine deaminase / : / DNA cytosine deamination / importin-alpha family protein binding / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Cytidine and dCMP deaminase domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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, 4items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytidine and dCMP deaminase domain-containing protein 1
B: Cytidine and dCMP deaminase domain-containing protein 1
C: Cytidine and dCMP deaminase domain-containing protein 1
D: Cytidine and dCMP deaminase domain-containing protein 1
E: Cytidine and dCMP deaminase domain-containing protein 1
F: Cytidine and dCMP deaminase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,50224
Polymers363,9146
Non-polymers3,58818
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cytidine and dCMP deaminase domain-containing protein 1 / Cytidine deaminase / Testis development protein NYD-SP15


Mass: 60652.320 Da / Num. of mol.: 6 / Mutation: E400A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDADC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BWV3, cytidine deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human CDADC1 hexamer with bound dCTP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.363 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 42.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 310460 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 19.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002218864
ELECTRON MICROSCOPYf_angle_d0.469625488
ELECTRON MICROSCOPYf_chiral_restr0.04032856
ELECTRON MICROSCOPYf_plane_restr0.00343192
ELECTRON MICROSCOPYf_dihedral_angle_d4.92172544

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