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- PDB-7d3w: Non-specific and specific interactions work cooperatively to prom... -

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Basic information

Entry
Database: PDB / ID: 7d3w
TitleNon-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A
Components
  • DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3')
  • DNA dC->dU-editing enzyme APOBEC-3A
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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-3A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsCao, C. / Liu, Y. / Lan, W.
CitationJournal: Protein Sci. / Year: 2022
Title: Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance.
Authors: Liu, Y. / Lan, W. / Wang, C. / Cao, C.
History
DepositionSep 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1243
Polymers26,0592
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1680 Å2
ΔGint-44 kcal/mol
Surface area14430 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3A / A3A / Phorbolin-1


Mass: 23049.896 Da / Num. of mol.: 1 / Mutation: L262N, C263S, E271Q, C370Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3A / Production host: Escherichia coli (E. coli)
References: UniProt: P31941, single-stranded DNA cytosine deaminase
#2: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3')


Mass: 3009.001 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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CA)CB
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D CBCA(CO)NH
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-15N TOCSY
181isotropic12D 1H-15N HSQC
192isotropic12D 1H-13C HSQC
1102isotropic13D 1H-13C NOESY aliphatic
1112isotropic13D 1H-13C NOESY aromatic
1122isotropic13D (H)CCH-TOCSY
1132isotropic22D filter TOCSY
1142isotropic22D filter NOESY
1151isotropic23D 15N-filter-edit NOESY
1162isotropic23D 13C-filter-edit NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution125 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA, 90% H2O/10% D2Olow concentration of complex to prevent aggregationA3A_complex90% H2O/10% D2O
solution225 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA, 100% D2Olow concentration of complex to prevent aggregationA3A_complex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphatenatural abundance1
200 mMsodium chloridenatural abundance1
50 uMZinc chloridenatural abundance1
5 mMDTTnatural abundance1
0.28 mMA3A[U-13C; U-15N]1
0.56 mMDNAnatural abundance1
25 mMsodium phosphatenatural abundance2
200 mMsodium chloridenatural abundance2
50 uMZinc chloridenatural abundance2
5 mMDTTnatural abundance2
0.28 mMA3A[U-13C; U-15N]2
0.56 mMDNAnatural abundance2
Sample conditionsIonic strength: 375 mM / Label: 1 / pH: 7.3 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Agilent DD2AgilentDD28002

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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