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 27977

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: 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:
UBXD1-PUB_domain, polymer, 119 residues, 13804 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

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

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

Data sets:
Data typeCount
13C chemical shifts535
15N chemical shifts117
1H chemical shifts811

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1UBXD1-PUB domain1

Entities:

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

Residues -4 to -1 represent a cloning artifact

1   GLYSERHISMETSERTHRASPPROVALALA
2   ALASERILEMETLYSILETYRTHRPHEASN
3   LYSASPGLNASPARGVALLYSLEUGLYVAL
4   ASPTHRILEALALYSTYRLEUASPASNILE
5   HISLEUHISPROGLUGLUGLULYSTYRARG
6   LYSILELYSLEUGLNASNLYSVALPHEGLN
7   GLUARGILEASNCYSLEUGLUGLYTHRHIS
8   GLUPHEPHEGLUALAILEGLYPHEGLNLYS
9   VALLEULEUPROALAGLNASPGLNGLUASP
10   PROGLUGLUPHETYRVALLEUSERGLUTHR
11   THRLEUALAGLNPROGLNSERLEUGLUARG
12   HISLYSGLUGLNLEULEUALAALAGLU

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D (H)C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HC(C)H-COSY aliphaticsample_2isotropicsample_conditions_1
3D HC(C)H-TOCSY aliphaticsample_2isotropicsample_conditions_1
3D HC(C)H-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D Histidin H(C)N-SOFAST-HMQCsample_1isotropicsample_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

Related Database Links:

UNP Q9BZV1
PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts