BMRB Entry 36404
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36404
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Solution structure of the C-clamp domain from human HDBP1 in complex with DNA PubMed: 33983734
Deposition date: 2021-01-04 Original release date: 2021-12-30
Authors: Duan, B.; Xia, B.
Citation: Duan, Bo; Fu, Dihong; Zhang, Chaoqun; Ding, Pengfei; Dong, Xianzhi; Xia, Bin. "Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains." J. Am. Chem. Soc. 143, 7688-7697 (2021).
Assembly members:
SLC2A4 regulator, polymer, 33 residues, 4032.811 Da.
DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3'), polymer, 11 residues, 3374.210 Da.
DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3'), polymer, 11 residues, 3334.186 Da.
ZINC ION, non-polymer, 65.409 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 K-12 Vector: pET-21b
Entity Sequences (FASTA):
SLC2A4 regulator: GDAKKCRKVYGMERRDLWCT
ACRWKKACQRFLD
DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3'): TATGCCGGGAC
DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3'): GTCCCGGCATA
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 121 |
| 15N chemical shifts | 40 |
| 1H chemical shifts | 450 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
| 3 | unit_3 | 3 |
| 4 | unit_4 | 4 |
Entities:
Entity 1, unit_1 33 residues - 4032.811 Da.
| 1 | GLY | ASP | ALA | LYS | LYS | CYS | ARG | LYS | VAL | TYR | ||||
| 2 | GLY | MET | GLU | ARG | ARG | ASP | LEU | TRP | CYS | THR | ||||
| 3 | ALA | CYS | ARG | TRP | LYS | LYS | ALA | CYS | GLN | ARG | ||||
| 4 | PHE | LEU | ASP |
Entity 2, unit_2 11 residues - 3374.210 Da.
| 1 | DT | DA | DT | DG | DC | DC | DG | DG | DG | DA | ||||
| 2 | DC |
Entity 3, unit_3 11 residues - 3334.186 Da.
| 1 | DG | DT | DC | DC | DC | DG | DG | DC | DA | DT | ||||
| 2 | DA |
Entity 4, unit_4 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: C-clamp, [U-13C; U-15N], 0.5 ± 0.01 mM; HD5-DNA_1 0.5 ± 0.01 mM; HD5-DNA_2 0.5 ± 0.01 mM; sodium phosphate 10 mM; NaCl 10 mM; H2O 95%; D2O, [U-2H], 5%
sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CCH-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D F1, F2-15N/13C-filtered 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D F1-15N/13C filtered, F2-15N edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D F1-15N/13C filtered, F2-13C edited NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, peak picking
SANE, Duggan, Legge, Dyson & Wright - data analysis
NMR spectrometers:
- Bruker AVANCE III HD 950 MHz
- Bruker AVANCE III HD 500 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts