BMRB Entry 25985
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR25985
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Title: NMR Structure of the C-Terminal Domain of human APOBEC3B PubMed: 27163633
Deposition date: 2016-03-08 Original release date: 2016-05-31
Authors: Byeon, In-Ja; Byeon, Chang-Hyeock; Gronenborn, Angela
Citation: Byeon, In-Ja; Byeon, Chang-Hyeock; Wu, Tiyun; Mitra, Mithun; Singer, Dustin; Levin, Judith; Gronenborn, Angela. "Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity" Biochemistry 55, 2944-2959 (2016).
Assembly members:
A3B-CTD, polymer, 205 residues, 24409.651 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
A3B-CTD: MEILRYLMDPDTFTFNFNND
PLVLRRRQTYLCYEVERLDN
GTWVLMDQHMGFLCNEAKNL
LCGFYGRHAELRFLDLVPSL
QLDPAQIYRVTWFISWSPCF
SWGCAGEVRAFLQENTHVRL
RIFAARIYDYDPLYKEALQM
LRDAGAQVSIMTYDEFEYCW
DTFVYRQGCPFQPWDGLEEH
SQALSGRLRAILQNQGNLEH
HHHHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 481 |
| 15N chemical shifts | 388 |
| 1H chemical shifts | 1359 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | A3B CTD | 1 |
Entities:
Entity 1, A3B CTD 205 residues - 24409.651 Da.
| 1 | MET | GLU | ILE | LEU | ARG | TYR | LEU | MET | ASP | PRO | ||||
| 2 | ASP | THR | PHE | THR | PHE | ASN | PHE | ASN | ASN | ASP | ||||
| 3 | PRO | LEU | VAL | LEU | ARG | ARG | ARG | GLN | THR | TYR | ||||
| 4 | LEU | CYS | TYR | GLU | VAL | GLU | ARG | LEU | ASP | ASN | ||||
| 5 | GLY | THR | TRP | VAL | LEU | MET | ASP | GLN | HIS | MET | ||||
| 6 | GLY | PHE | LEU | CYS | ASN | GLU | ALA | LYS | ASN | LEU | ||||
| 7 | LEU | CYS | GLY | PHE | TYR | GLY | ARG | HIS | ALA | GLU | ||||
| 8 | LEU | ARG | PHE | LEU | ASP | LEU | VAL | PRO | SER | LEU | ||||
| 9 | GLN | LEU | ASP | PRO | ALA | GLN | ILE | TYR | ARG | VAL | ||||
| 10 | THR | TRP | PHE | ILE | SER | TRP | SER | PRO | CYS | PHE | ||||
| 11 | SER | TRP | GLY | CYS | ALA | GLY | GLU | VAL | ARG | ALA | ||||
| 12 | PHE | LEU | GLN | GLU | ASN | THR | HIS | VAL | ARG | LEU | ||||
| 13 | ARG | ILE | PHE | ALA | ALA | ARG | ILE | TYR | ASP | TYR | ||||
| 14 | ASP | PRO | LEU | TYR | LYS | GLU | ALA | LEU | GLN | MET | ||||
| 15 | LEU | ARG | ASP | ALA | GLY | ALA | GLN | VAL | SER | ILE | ||||
| 16 | MET | THR | TYR | ASP | GLU | PHE | GLU | TYR | CYS | TRP | ||||
| 17 | ASP | THR | PHE | VAL | TYR | ARG | GLN | GLY | CYS | PRO | ||||
| 18 | PHE | GLN | PRO | TRP | ASP | GLY | LEU | GLU | GLU | HIS | ||||
| 19 | SER | GLN | ALA | LEU | SER | GLY | ARG | LEU | ARG | ALA | ||||
| 20 | ILE | LEU | GLN | ASN | GLN | GLY | ASN | LEU | GLU | HIS | ||||
| 21 | HIS | HIS | HIS | HIS | HIS |
Samples:
2H_13C_15N_A3B-CTD: A3B-CTD, [U-13C; U-15N; U-2H], 0.08 mM; Zinc 0.08 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM
13C_15N_A3B-CTD: A3B-CTD, [U-100% 13C; U-100% 15N], 0.08 mM; Zinc 0;08 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM
A3B-CTD_3: A3B-CTD 0.05 mM; Zinc 0.05 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM
H2O: ionic strength: 25 mM; pH: 6.9; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | 2H_13C_15N_A3B-CTD | isotropic | H2O |
| 3D HNCA | 13C_15N_A3B-CTD | isotropic | H2O |
| 3D HNCACB | 2H_13C_15N_A3B-CTD | isotropic | H2O |
| 3D HN(CO)CACB | 2H_13C_15N_A3B-CTD | isotropic | H2O |
| 2D 1H-15N HSQC | 13C_15N_A3B-CTD | isotropic | H2O |
| 3D simultaneous 13C- and 15N-edited NOESY | 13C_15N_A3B-CTD | isotropic | H2O |
| 3D TROSY-HNCACB | 2H_13C_15N_A3B-CTD | isotropic | H2O |
| 3D TROSY-HN(CO)CACB | 2H_13C_15N_A3B-CTD | isotropic | H2O |
| 2D 1H-1H NOESY | A3B-CTD_3 | isotropic | H2O |
| 3D HCCH-TOCSY | 13C_15N_A3B-CTD | isotropic | H2O |
| 2D 1H-13C HSQC | 13C_15N_A3B-CTD | isotropic | H2O |
Software:
CcpNmr_Analysis v2.2, CCPN - chemical shift assignment, data analysis, peak picking
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 900 MHz
- Bruker Avance 700 MHz
- Bruker Avance 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts