BMRB Entry 36404

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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

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Title:
Solution structure of the C-clamp domain from human HDBP1 in complex with DNA
Deposition date:
2021-01-04
Original release date:
2021-12-30
Authors:
Duan, B.; Xia, B.
Citation:

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).
PubMed: 33983734

Assembly members:

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:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli K-12   Vector: pET-21b

Entity Sequences (FASTA):

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

Data typeCount
13C chemical shifts121
15N chemical shifts40
1H chemical shifts450

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33
4unit_44

Entities:

Entity 1, unit_1 33 residues - 4032.811 Da.

1   GLYASPALALYSLYSCYSARGLYSVALTYR
2   GLYMETGLUARGARGASPLEUTRPCYSTHR
3   ALACYSARGTRPLYSLYSALACYSGLNARG
4   PHELEUASP

Entity 2, unit_2 11 residues - 3374.210 Da.

1   DTDADTDGDCDCDGDGDGDA
2   DC

Entity 3, unit_3 11 residues - 3334.186 Da.

1   DGDTDCDCDCDGDGDCDADT
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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D CCH-COSYsample_1isotropicsample_conditions_1
2D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D F1, F2-15N/13C-filtered 1H-1H NOESYsample_1isotropicsample_conditions_1
3D F1-15N/13C filtered, F2-15N edited NOESYsample_1isotropicsample_conditions_1
3D F1-15N/13C filtered, F2-13C edited NOESYsample_1isotropicsample_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 peaks
SPARKY: Backbone or all simulated peaks