BMRB Entry 16882

Name: Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota
Published: 2010-06-15

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PDB ID: 2khu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16882
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Nicholas Rego and David Koes
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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 Motif of Human Polymerase Iota

Deposition date:

2010-04-19

Original release date:

2010-06-15

Authors:

Bomar, Martha; D'Souza, Sanjay; Bienko, Marzena; Dikic, Ivan; Walker, Graham

Citation:

Citation: Bomar, Martha; Bienko, Sanjay; Dikic, Marzena; Walker, Ivan; Zhou, Graham. "Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1." Mol. Cell 37, 408-417 (2010).
PubMed: 20159559

Assembly members:

Assembly members:
Ubiquitin-Binding Motif, polymer, 108 residues, 3753.299 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 Vector: pET30-GB1-fusion

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin-Binding Motif: MQYKLILNGKTLKGETTTEA VDAATAEKVFKQYANDNGVD GEWTYDDATKTFTVTEGSDE KITFPSDIDPQVFYELPEAV QKELLAEWKRTGSDFHIGHK LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	435
15N chemical shifts	103
1H chemical shifts	694

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	UBM2	1

Entities:

Entity 1, UBM2 108 residues - 3753.299 Da.

Residues 1-56 represent the GB1-tag. Residues 57-58, 101-108 are cloning artifacts (including the His6-tag)

1

MET

GLN

TYR

LYS

LEU

ILE

LEU

ASN

GLY

LYS

2

THR

LEU

LYS

GLY

GLU

THR

GLU

ALA

3

VAL

ASP

ALA

THR

ALA

GLU

LYS

VAL

PHE

4

LYS

GLN

TYR

ALA

ASN

ASP

ASN

GLY

VAL

ASP

5

GLY

GLU

TRP

THR

TYR

ASP

ALA

THR

LYS

6

THR

PHE

THR

VAL

THR

GLU

GLY

SER

ASP

GLU

7

LYS

ILE

THR

PHE

PRO

SER

ASP

ILE

ASP

PRO

8

GLN

VAL

PHE

TYR

GLU

LEU

PRO

GLU

ALA

VAL

9

GLN

LYS

GLU

LEU

ALA

GLU

TRP

LYS

ARG

10

THR

GLY

SER

ASP

PHE

HIS

ILE

GLY

HIS

LYS

11

LEU

GLU

HIS

Samples:

sample_1: UBM2, [U-100% 13C; U-100% 15N], 1 – 4 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

X-PLOR NIH v2.19, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 600 MHz

BMRB	15156 15380 16444 16627 16873 17810 18397 26630
PDB	1GB1 1PGA 1PGB 1PN5 2CWB 2DEN 2GB1 2GI9 2I2Y 2I38 2JSV 2JU6 2K0P 2KBT 2KHU 2KHW 2KLK 2KN4 2KQ4 2KWD 2LGI 2QMT 2RMM 3GB1 3MP9 4Q0C