BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15160

Title: Solution Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Y-Polymerase Eta   PubMed: 17304240

Authors: Bomar, Martha; Zhou, Pei

Citation: Bomar, Martha; Pai, Ming-Tao; Tzeng, Shiou-Ru; Li, Shawn Shun-Cheng; Zhou, Pei. "Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta"  EMBO Rep. 8, 247-251 (2007).

Assembly members:
UBZ_domain, polymer, 39 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
UBZ_domain: GSHMAAEDQVPCEKCGSLVP VWDMPEHMDYHFALELQKS

Data sets:
Data typeCount
13C chemical shifts126
15N chemical shifts36
1H chemical shifts258

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1UBZ domain1
2ZINC ION2

Entities:

Entity 1, UBZ domain 39 residues - Formula weight is not available

corresponding to GSHM due to coloning stategy plus residues 628-662 of human polymerase eta

1   GLYSERHISMETALAALAGLUASPGLNVAL
2   PROCYSGLULYSCYSGLYSERLEUVALPRO
3   VALTRPASPMETPROGLUHISMETASPTYR
4   HISPHEALALEUGLULEUGLNLYSSER

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: UBZ domain, [U-100% 15N], 2 mM; phosphate 25 mM; KCL 100 mM

sample_2: UBZ domain, [U-100% 13C; U-100% 15N], 2 mM; phosphate 25 mM; KCL 100 mM

sample_3: UBZ domain, [U-10% 13C; U-100% 15N], 2 mM; phosphate 25 mM; KCL 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HN(COCA)CBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

PDB
REF XP_004408176 XP_011815748 XP_011815749