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- PDB-2kem: Extended structure of citidine deaminase domain of APOBEC3G -

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Basic information

Entry
Database: PDB / ID: 2kem
TitleExtended structure of citidine deaminase domain of APOBEC3G
ComponentsDNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE / helix / sheet / 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 / 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)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHarjes, E. / Gross, P.J. / Chen, K. / Lu, Y. / Shindo, K. / Nowarski, R. / Gross, J.D. / Kotler, M. / Harris, R.S. / Matsuo, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model
Authors: Harjes, E. / Gross, P.J. / Chen, K.M. / Lu, Y. / Shindo, K. / Nowarski, R. / Gross, J.D. / Kotler, M. / Harris, R.S. / Matsuo, H.
History
DepositionJan 30, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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)23,5802
Polymers23,5141
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 23514.463 Da / Num. of mol.: 1 / Fragment: UNP residues 191-284 / Mutation: L44K, C53A, F120K, C131A, C166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3(RIL)
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 / Details: citidine deaminase, zinc containing
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HN(CA)CB
1433D 1H-15N NOESY
1513D 1H-15N NOESY
1643D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] apobec3g-1, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-13C; U-15N; U-2H] apobec3g-2, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-15N; U-50% 2H] apobec3g-3, 90% H2O/10% D2O90% H2O/10% D2O
40.3 mM [U-100% 13C] apobec3g-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMapobec3g-1[U-100% 15N]1
0.3 mMapobec3g-2[U-13C; U-15N; U-2H]2
0.3 mMapobec3g-3[U-15N; U-50% 2H]3
0.3 mMapobec3g-4[U-100% 13C]4
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Varian INOVAVarianINOVA8002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004
Varian INOVAVarianINOVA6005

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: cns
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1

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