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- PDB-3iqs: Crystal structure of the anti-viral APOBEC3G catalytic domain -

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Basic information

Entry
Database: PDB / ID: 3iqs
TitleCrystal structure of the anti-viral APOBEC3G catalytic domain
ComponentsDNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE / FIVE BETA-STRANDS SURROUNDED BY SIX ALPHA-HELICES / ALTERNATIVE SPLICING / ANTIVIRAL DEFENSE / CYTOPLASM / HOST-VIRUS INTERACTION / METAL-BINDING / NUCLEUS / POLYMORPHISM / UBL CONJUGATION / ZINC
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 / cytidine deaminase activity / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...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 / cytidine deaminase activity / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / 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
APOBEC-like C-terminal domain / 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
DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHolden, L.G. / Prochnow, C. / Chang, Y.P. / Bransteitter, R. / Chelico, L. / Sen, U. / Stevens, R.C. / Goodman, R.F. / Chen, X.S.
CitationJournal: Nature / Year: 2008
Title: Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications.
Authors: Holden, L.G. / Prochnow, C. / Chang, Y.P. / Bransteitter, R. / Chelico, L. / Sen, U. / Stevens, R.C. / Goodman, M.F. / Chen, X.S.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1532
Polymers22,0881
Non-polymers651
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.464, 57.329, 40.578
Angle α, β, γ (deg.)90.00, 96.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein / ARP-9 / CEM-15 / CEM15


Mass: 22087.990 Da / Num. of mol.: 1 / Fragment: APOBEC3G Catalytic Domain (UNP residues 197-380)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90
References: UniProt: Q9HC16, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH 6.5, 40% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792060, 0.9790670
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792061
20.9790671
ReflectionResolution: 2.2→50 Å / Num. all: 18902 / Num. obs: 17604 / % possible obs: 93.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.28 Å

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / σ(F): 1.7 / Stereochemistry target values: Engh & Huber
Details: 1. The Friedel pairs were used in phasing. 2. Authors state that the main difference between the old (3E1U, see remark 900) and this entry is that the conformation of four residues (residues ...Details: 1. The Friedel pairs were used in phasing. 2. Authors state that the main difference between the old (3E1U, see remark 900) and this entry is that the conformation of four residues (residues 268-271) of a loop on the surface is readjusted.
RfactorNum. reflectionSelection details
Rfree0.263 1511 random
Rwork0.251 --
obs0.251 15669 -
all-16598 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 1 28 1552

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