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 16114

Title: Solution structure of a Ubiquitin/UIM fusion protein   PubMed: 20053359

Deposition date: 2009-01-09 Original release date: 2010-02-11

Authors: Sgourakis, Nikolaos; Patel, Mayank; Garcia, Angel; Makhatadze, George; McCallum, Scott

Citation: Sgourakis, Nikolaos; Patel, Mayank; Garcia, Angel; Makhatadze, George; McCallum, Scott. "Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain."  J. Mol. Biol. 396, 1128-1144 (2010).

Assembly members:
Ubiquitin/UIM_fusion_protein, polymer, 114 residues, Formula weight is not available

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

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

Entity Sequences (FASTA):
Ubiquitin/UIM_fusion_protein: MHHHHHHGEFQIFAKTLTGK TITLEVESSDTIDNVKSKIQ DKEGIPPDQQRLIWAGKQLE DGRTLSDYNIQRESTLHLVL RLRGGSMGGAADEEELIRKA IELSLKESRNSGGY

Data sets:
Data typeCount
13C chemical shifts324
15N chemical shifts105
1H chemical shifts684

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ubiquitin/UIM fusion protein1

Entities:

Entity 1, Ubiquitin/UIM fusion protein 114 residues - Formula weight is not available

1   METHISHISHISHISHISHISGLYGLUPHE
2   GLNILEPHEALALYSTHRLEUTHRGLYLYS
3   THRILETHRLEUGLUVALGLUSERSERASP
4   THRILEASPASNVALLYSSERLYSILEGLN
5   ASPLYSGLUGLYILEPROPROASPGLNGLN
6   ARGLEUILETRPALAGLYLYSGLNLEUGLU
7   ASPGLYARGTHRLEUSERASPTYRASNILE
8   GLNARGGLUSERTHRLEUHISLEUVALLEU
9   ARGLEUARGGLYGLYSERMETGLYGLYALA
10   ALAASPGLUGLUGLULEUILEARGLYSALA
11   ILEGLULEUSERLEULYSGLUSERARGASN
12   SERGLYGLYTYR

Samples:

sample_1: Ubiquitin/UIM fusion protein, [U-100% 13C; U-100% 15N], 1.24 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_2: Ubiquitin/UIM fusion protein, [U-100% 15N], 1.1 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_3: Ubiquitin/UIM fusion protein, [U-100% 15N], 0.5 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.103 M; pH: 6; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
2D HN-IPAPsample_3anisotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D (H)C(CCO)NH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3anisotropicsample_conditions_1
2D HN-IPAPsample_2anisotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - processing

SPARKY v3.111, Goddard - chemical shift assignment, data analysis, peak picking

X-PLOR v2.18, Brunger - data analysis, geometry optimization, refinement, structure solution

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis, structure solution

PALES, Markus Zweckstetter and Ad Bax - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAO40007
EMBL CDO91688
GB KGQ91175 KGR10456 KGT69098 KGU29735 KHC54981

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