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- PDB-2nbq: NMR Structure of the C-Terminal Domain of human APOBEC3B -

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Basic information

Entry
Database: PDB / ID: 2nbq
TitleNMR Structure of the C-Terminal Domain of human APOBEC3B
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE
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 / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / 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-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsByeon, I.L. / Byeon, C. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.
Authors: Byeon, I.J. / Byeon, C.H. / Wu, T. / Mitra, M. / Singer, D. / Levin, J.G. / Gronenborn, A.M.
History
DepositionMar 9, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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_database_remark.text / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5012
Polymers24,4361
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 256structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 24435.691 Da / Num. of mol.: 1 / Fragment: residues 187-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q9UH17, 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: NMR Structure of the APOBEC3B Catalytic Domain: Structural Bais for Substrate Binding and DNA Deaminase Activity
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1313D HN(CA)CB
1413D HN(COCA)CB
1522D 1H-15N HSQC
1623D simultaneous 13C- and 15N-edited NOESY
1713D TROSY-HN(CA)CB
1813D TROSY-HN(CO)CACB
1932D 1H-1H NOESY
11023D (H)CCH-TOCSY
11122D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.08 mM [U-13C; U-15N; U-2H] A3B_CTD, 0.08 mM Zinc, 10 mM DTT, 25 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
20.08 mM [U-100% 13C; U-100% 15N] A3B_CTD, 0.08 mM Zinc, 10 mM DTT, 25 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
30.05 mM A3B_CTD, 0.05 mM Zinc, 10 mM DTT, 25 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.08 mMA3B_CTD-1[U-13C; U-15N; U-2H]1
0.08 mMZinc-21
7 %D2O-3[U-100% 2H]1
93 %H2O-41
10 mMDTT-51
25 mMsodium phosphate-61
0.08 mMA3B_CTD-7[U-100% 13C; U-100% 15N]2
0.08 mMZinc-82
7 %D2O-9[U-100% 2H]2
93 %H2O-102
10 mMDTT-112
25 mMsodium phosphate-122
0.05 mMA3B_CTD-133
0.05 mMZinc-143
7 %D2O-15[U-100% 2H]3
93 %H2O-163
10 mMDTT-173
25 mMsodium phosphate-183
Sample conditionsIonic strength: 0 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorepeak picking
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FLEXIBLE (HEXA-HISTIDINE TAG) RESIDUES WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND THUS NOT SHOWN IN THE COORDINATES.
NMR constraintsHydrogen bond constraints total count: 168 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 155 / Protein psi angle constraints total count: 154
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.397 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 30 / Maximum lower distance constraint violation: 0.5 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.031 Å / Distance rms dev error: 0.002 Å

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