BMRB Entry 27977

Name: Solution structure of the PUB domain of human UBXD1 protein
Published: 2019-12-17

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PDB ID: 6sap
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27977
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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:

Solution structure of the PUB domain of human UBXD1 protein

Deposition date:

2019-07-17

Original release date:

2019-12-17

Authors:

Beuck, Christine; Bayer, Peter; Blueggel, Mike

Citation:

Citation: Blueggel, Mike; van den Boom, Johannes; Meyer, Hemmo; Bayer, Peter; Beuck, Christine. "Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase" Biomolecules 9, 876-876 (2019).

Assembly members:

Assembly members:
UBXD1-PUB_domain, polymer, 119 residues, 13804 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UBXD1-PUB_domain: GSHMSTDPVAASIMKIYTFN KDQDRVKLGVDTIAKYLDNI HLHPEEEKYRKIKLQNKVFQ ERINCLEGTHEFFEAIGFQK VLLPAQDQEDPEEFYVLSET TLAQPQSLERHKEQLLAAE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	535
15N chemical shifts	117
1H chemical shifts	811

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	UBXD1-PUB domain	1

Entities:

Entity 1, UBXD1-PUB domain 119 residues - 13804 Da.

Residues -4 to -1 represent a cloning artifact

1

GLY

SER

HIS

MET

SER

THR

ASP

PRO

VAL

ALA

2

ALA

SER

ILE

MET

LYS

ILE

TYR

THR

PHE

ASN

3

LYS

ASP

GLN

ASP

ARG

VAL

LYS

LEU

GLY

VAL

4

ASP

THR

ILE

ALA

LYS

TYR

LEU

ASP

ASN

ILE

5

HIS

LEU

HIS

PRO

GLU

LYS

TYR

ARG

6

LYS

ILE

LYS

LEU

GLN

ASN

LYS

VAL

PHE

GLN

7

GLU

ARG

ILE

ASN

CYS

LEU

GLU

GLY

THR

HIS

8

GLU

PHE

GLU

ALA

ILE

GLY

PHE

GLN

LYS

9

VAL

LEU

PRO

ALA

GLN

ASP

GLN

GLU

ASP

10

PRO

GLU

PHE

TYR

VAL

LEU

SER

GLU

THR

11

THR

LEU

ALA

GLN

PRO

GLN

SER

LEU

GLU

ARG

12

HIS

LYS

GLU

GLN

LEU

ALA

GLU

Samples:

sample_1: UBXD1-PUB domain, [U-98% 13C; U-98% 15N], 600-900 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; H2O 90%; D2O, [U-2H], 10%; DSS 0.1 mM

sample_2: UBXD1-PUB domain, [U-98% 13C; U-98% 15N], 500 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; D2O, [U-99% 2H], 100%; DSS 0.1 mM

sample_3: UBXD1-PUB domain, [U-98% 15N], 700 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; H2O 90%; D2O, [U-2H], 10%; DSS 0.1 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D (H)C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D HC(C)H-COSY aliphatic	sample_2	isotropic	sample_conditions_1
3D HC(C)H-TOCSY aliphatic	sample_2	isotropic	sample_conditions_1
3D HC(C)H-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D Histidin H(C)N-SOFAST-HMQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN vV. 3.5, Bruker Biospin - collection, processing

CARA v1.6, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

UNIO v10, Herrmann - NOE assignment, NOESY peak picking

CYANA v3.98.9, Guntert, Mumenthaler and Wuthrich - structure solution

YASARA v11.12.31, Krieger - refinement

NMR spectrometers:

Bruker Avance 700 MHz

UNP	Q9BZV1
PDB	6SAP
AlphaFold	Q9BZV0