BMRB Entry 15160

Name: Solution Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Y-Polymerase Eta
Published: 2007-03-06

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PDB ID: 2i5o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15160
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2007-03-06

Original release date:

2007-03-06

Authors:

Bomar, Martha; Zhou, Pei

Citation:

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).
PubMed: 17304240

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UBZ_domain: GSHMAAEDQVPCEKCGSLVP VWDMPEHMDYHFALELQKS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	126
15N chemical shifts	36
1H chemical shifts	258

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	UBZ domain	1
2	ZINC ION	2

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

GLY

SER

HIS

MET

ALA

GLU

ASP

GLN

VAL

2

PRO

CYS

GLU

LYS

CYS

GLY

SER

LEU

VAL

PRO

3

VAL

TRP

ASP

MET

PRO

GLU

HIS

MET

ASP

TYR

4

HIS

PHE

ALA

LEU

GLU

LEU

GLN

LYS

SER

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_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

PDB	2I5O
REF	XP_004408176 XP_011815748 XP_011815749