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- PDB-6k3j: Solution structure of APOBEC3G-CD2 with ssDNA, Product A -

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Basic information

Entry
Database: PDB / ID: 6k3j
TitleSolution structure of APOBEC3G-CD2 with ssDNA, Product A
Components
  • DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')
  • DNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE/DNA / APOBEC3G / DNA cytidine deaminase complex with DNA / HYDROLASE-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 / 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 / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsCao, C. / Yan, X. / Lan, W. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21778065 China
CitationJournal: Chem Asian J / Year: 2019
Title: Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA.
Authors: Yan, X. / Lan, W. / Wang, C. / Cao, C.
History
DepositionMay 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3343
Polymers25,2692
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2860 Å2
ΔGint-48 kcal/mol
Surface area13260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / 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


Mass: 22161.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HC16, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')


Mass: 3106.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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-IDSample stateSpectrometer-IDType
113anisotropic13D HNCO
123anisotropic13D HNCA
133anisotropic13D HN(CO)CA
143anisotropic13D HN(CA)CB
151anisotropic12D 1H-15N HSQC
162anisotropic43D 1H-13C NOESY aliphatic
172anisotropic43D 1H-13C NOESY aromatic
181anisotropic23D 1H-15N NOESY
192anisotropic43D (H)CCH-TOCSY
1141anisotropic23D 1H-15N TOCSY
1102anisotropic42D 1H-13C HSQC aliphatic
1112anisotropic42D 1H-13C HSQC aromatic
1124anisotropic32D DQF-COSY
1134anisotropic32D 1H-1H TOCSY
1154anisotropic32D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION, 90% H2O/10% D2O13C,15N_sample90% H2O/10% D2O
solution20.35 mM [U-99% 13C; U-99% 15N] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION, 100% D2O13C,15N_sample_2100% D2O
solution30.35 mM [U-100% 13C; U-100% 15N; U-80% 2H] DNA dC->dU-editing enzyme APOBEC3G, 0.525 mM DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 50 uM ZINC ION, 90% H2O/10% D2O13C,15N,2H_sample90% H2O/10% D2O
solution41 mM DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2OssDNA90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMDNA dC->dU-editing enzyme APOBEC3G[U-99% 13C; U-99% 15N]1
0.525 mMDNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')natural abundance1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
50 uMZINC IONnatural abundance1
0.35 mMDNA dC->dU-editing enzyme APOBEC3G[U-99% 13C; U-99% 15N]2
0.525 mMDNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')natural abundance2
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
50 uMZINC IONnatural abundance2
0.35 mMDNA dC->dU-editing enzyme APOBEC3G[U-100% 13C; U-100% 15N; U-80% 2H]3
0.525 mMDNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')natural abundance3
50 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
5 mMDTTnatural abundance3
50 uMZINC IONnatural abundance3
1 mMDNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3')natural abundance4
50 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCE IIIBrukerAVANCE III9004
Varian UNITYVarianUNITY6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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