BMRB Entry 25382

Name: UBX-L domain of VCIP135
Published: 2016-07-11

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PDB ID: 2mx2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25382
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

UBX-L domain of VCIP135

Deposition date:

2014-12-07

Original release date:

2016-07-11

Authors:

Iwazu, Takahiro; Murayama, Shuhei; Igarashi, Ryuji; Hrioaki, Hidekazu; Shirakawa, Masahiro; Tochio, Hidehito

Citation:

Citation: Iwazu, Takahiro; Murayama, Shuhei; Igarashi, Ryuji; Hrioaki, Hidekazu; Shirakawa, Masahiro; Tochio, Hidehito. "Structure and interaction mode of the UBX-L domain of VCIP135 determined by solution NMR spectroscopy" Sci. Rep. ., .-..

Assembly members:

Assembly members:
VCIP135 UBX, polymer, 86 residues, 9331.919 Da.

Natural source:

Natural source: Common Name: Norway Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-4T3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VCIP135 UBX: GSDHSKEKKIRITTNDGRQS MVTLKSSTTFFELQESIARE FNIPPYLQCIRYGFPPKELM PPQAGMEKEPVPLQHGDRIT IEILKG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	316
15N chemical shifts	79
1H chemical shifts	638

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VCIP135 UBX	1

Entities:

Entity 1, VCIP135 UBX 86 residues - 9331.919 Da.

1

GLY

SER

ASP

HIS

SER

LYS

GLU

LYS

ILE

2

ARG

ILE

THR

ASN

ASP

GLY

ARG

GLN

SER

3

MET

VAL

THR

LEU

LYS

SER

THR

PHE

4

PHE

GLU

LEU

GLN

GLU

SER

ILE

ALA

ARG

GLU

5

PHE

ASN

ILE

PRO

TYR

LEU

GLN

CYS

ILE

6

ARG

TYR

GLY

PHE

PRO

LYS

GLU

LEU

MET

7

PRO

GLN

ALA

GLY

MET

GLU

LYS

GLU

PRO

8

VAL

PRO

LEU

GLN

HIS

GLY

ASP

ARG

ILE

THR

9

ILE

GLU

ILE

LEU

LYS

GLY

Samples:

sample_1: VCIP135 UBX, [U-13C; U-15N], 1.86 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	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
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker DRX 700 MHz
Bruker DPX 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks