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- PDB-5zva: APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) -

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Basic information

Entry
Database: PDB / ID: 5zva
TitleAPOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
Components
  • APEBEC3F/ssDNA-C9
  • DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*CP*T)-3')
KeywordsSTRUCTURAL PROTEIN/DNA / APOBEC3F / HIV-1 / deamination / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / P-body / Vif-mediated degradation of APOBEC3G / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Novel AID APOBEC clade 2 / 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
CACODYLATE ION / DNA / DNA dC->dU-editing enzyme APOBEC-3F / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA-binding vector pODB80 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCheng, C. / Zhang, T.L. / Wang, C.X. / Lan, W.X. / Ding, J.P. / Cao, C.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)91753119, 21778065 and 21472229 China
CitationJournal: Chin.J.Chem. / Year: 2018
Title: Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA
Authors: Cheng, C. / Zhang, T. / Wang, C. / Lan, W. / Ding, J. / Cao, C.
History
DepositionMay 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / struct
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APEBEC3F/ssDNA-C9
B: APEBEC3F/ssDNA-C9
C: DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2387
Polymers52,8343
Non-polymers4054
Water2,072115
1
A: APEBEC3F/ssDNA-C9
C: DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1164
Polymers27,9142
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-42 kcal/mol
Surface area11810 Å2
MethodPISA
2
B: APEBEC3F/ssDNA-C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1223
Polymers24,9201
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-34 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.312, 91.304, 91.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein APEBEC3F/ssDNA-C9 / APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / ...APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein 9 / ARP-9 / CEM-15 / CEM15 / Deoxycytidine deaminase / A3G / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F / A3F


Mass: 24919.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes ...Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F)(reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J)
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019, APOBEC3F
Production host: prokaryotic environmental samples (environmental samples)
References: UniProt: Q9HC16, UniProt: Q8IUX4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*CP*T)-3')


Mass: 2993.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) DNA-binding vector pODB80 (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol(MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→45.68 Å / Num. obs: 23245 / % possible obs: 98.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.619

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASESphasing
PDB_EXTRACT3.24data extraction
ADDREFdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→45.68 Å / SU B: 12.618 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1158 5 %RANDOM
Rwork0.161 ---
obs0.164 21994 98.7 %-
Displacement parametersBiso mean: 50.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å20 Å20 Å2
2--2.18 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 178 16 115 3415
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07680.0152-0.05740.1379-0.04880.0540.0052-0.00450.00730.0048-0.007-0.0087-0.00180.0050.00180.07390.0001-0.00520.0009-0.00070.039-22.3506-5.428-4.0854
20.035-0.05470.00390.0862-0.01580.169-0.0037-0.0033-0.00170.00410.0057-0.00020.0025-0.0016-0.0020.0714-0.00090.00030.0005-0.00210.0385-8.2109-28.495628.923
36.56910.582.21160.2317-0.23781.78470.03590.0257-0.3485-0.1495-0.0081-0.06760.37150.042-0.02770.1752-0.03540.02970.0457-0.00230.0367-30.9308-26.919612.6758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -32 through 373 )
2X-RAY DIFFRACTION2chain 'B' and (resid -29 through 373 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 10 )

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