+Open data
-Basic information
Entry | Database: PDB / ID: 3iqs | ||||||
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Title | Crystal structure of the anti-viral APOBEC3G catalytic domain | ||||||
Components | DNA dC->dU-editing enzyme APOBEC-3G | ||||||
Keywords | HYDROLASE / 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 / deoxycytidine deaminase activity / cytidine deaminase activity / 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 / deoxycytidine deaminase activity / cytidine deaminase activity / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Holden, L.G. / Prochnow, C. / Chang, Y.P. / Bransteitter, R. / Chelico, L. / Sen, U. / Stevens, R.C. / Goodman, R.F. / Chen, X.S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iqs.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iqs.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 3iqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqs ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792060, 0.9790670 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2007 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. all: 18902 / Num. obs: 17604 / % possible obs: 93.1 % / Observed criterion σ(I): -3 | |||||||||
Reflection shell | Resolution: 2.2→2.28 Å |
-Processing
Software |
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Refinement | Method 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.
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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