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- PDB-2jyw: Solution structure of C-terminal domain of APOBEC3G -

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Basic information

Entry
Database: PDB / ID: 2jyw
TitleSolution structure of C-terminal domain of APOBEC3G
ComponentsDNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE / Protein / Zinc / Alternative splicing / Antiviral defense / Cytoplasm / Host-virus interaction / Metal-binding / Nucleus / Polymorphism / Ubl conjugation
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
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)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsC-terminal domain of APOBEC3G
AuthorsChen, K. / Harjes, E. / Gross, P.J. / Fahmy, A. / Lu, Y. / Shindo, K. / Harris, R.S. / Matsuo, H.
CitationJournal: Nature / Year: 2008
Title: Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G.
Authors: Chen, K.M. / Harjes, E. / Gross, P.J. / Fahmy, A. / Lu, Y. / Shindo, K. / Harris, R.S. / Matsuo, H.
History
DepositionDec 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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)22,7832
Polymers22,7171
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100lowest energy, ramachandran parameters
RepresentativeModel #1closest to the average

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Components

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


Mass: 22717.479 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: L37K, C46A, F113K, C124A, C159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G / Plasmid: pGEX6P2_A3G198-384 / Production host: Escherichia coli (E. coli)
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HN(CO)CA
1723D H(CCO)NH
1823D HN(CA)CO
1923D HN(COCA)CB
11023D C(CO)NH
11123D (H)CCH-TOCSY
11233D 1H-15N NOESY
11323D 1H-13C NOESY
11413D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 mM [U-100% 15N] Apobec3G, 95% H2O/5% D2O95% H2O/5% D2O
2300 mM [U-100% 13C; U-100% 15N; 80% 2H] Apobec3G, 95% H2O/5% D2O95% H2O/5% D2O
3300 mM [U-100% 15N, 80%2H] Apobec3G, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMApobec3G[U-100% 15N]1
300 mMApobec3G[U-100% 13C; U-100% 15N; 80% 2H]2
300 mMApobec3G[U-100% 15N, 80%2H]3
Sample conditionsIonic strength: 0 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, A.T. et al.refinement
CARA1.8.3Keller, R. et al.data analysis
CARA1.8.3Keller, R. et al.chemical shift assignment
NMRDraw2.5Delaglio, F. et al.processing
NMRDraw2.5Delaglio, F. et al.chemical shift assignment
Atnos/Candid1.1Herrmann, T. et al.structure solution
Atnos/Candid1.1Herrmann, T. et al.chemical shift assignment
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2008 / NOE intraresidue total count: 242 / NOE long range total count: 656 / NOE medium range total count: 506 / NOE sequential total count: 604 / Hydrogen bond constraints total count: 142 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 115
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest energy, ramachandran parameters
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 4.03 ° / Maximum upper distance constraint violation: 0.21 Å

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