BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 11547

Title: the pure alternative state of ubiquitin   PubMed: 24401037

Authors: Kitazawa, Soichiro; Kameda, Tomoshi; Kumo, Ayumi; Utsumi, Maho; Baxter, Nicola; Kato, Koichi; Williamson, Mike; Kitahara, Ryo

Citation: Kitazawa, Soichiro; Kameda, Tomoshi; Kumo, Ayumi; Utsumi, Maho; Baxter, Nicola; Kato, Koichi; Williamson, Mike; Kitahara, Ryo. "Close identity between the alternatively folded state N2 of ubiquitin and the conformation of the protein bound to ubiquitin-activating enzyme"  Biochemistry 53, 447-449 (2014).

Assembly members:
ubiquitin, polymer, 76 residues, 8562.888 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):
ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ NRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts337
15N chemical shifts79
1H chemical shifts564

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ubiquitin1

Entities:

Entity 1, ubiquitin 76 residues - 8562.888 Da.

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   ASNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Samples:

sample_1: ubiquitin, [U-100% 13C; U-100% 15N], 2 mM; Tris(hydroxymethyl)aminomethane, [U-100% 2H], 20 mM; DSS 0.2 mM; H2O 88%; D2O 12%

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 2500 bar; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D HNCOsample_1isotropicsample_conditions_1
3D 1H-13C/15N simultaneous evolutio NOESY HSQCsample_1isotropicsample_conditions_1

Software:

CYANA v3.93, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - peak picking

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

BMRB 11505 15047 15410 15689 15907 16582 16626 16895 17181 17439 17769 17919 18582 18583 18584 18610 18611 18737 19406 19412 25070 25123 26604 4245 4375
PDB
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA25706 CAA26488 CAA28495 CAA30815 CAA35999
GB AAA28997 AAA28998 AAA28999 AAA29000 AAA29001
PIR I50437 I51568 I65237 S13928 S21083
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
REF NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P0C273 P0C275 P0C276 P0CG47 P0CG48
TPE CEL68433 CEL70397 CEL75964 CEL78064
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295