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 11505

Title: Alternative structure of Ubiquitin   PubMed: 23421577

Authors: Kitazawa, Soichiro; Kameda, Tomoshi; Yagi-Utsumi, Maho; Kato, Koichi; Kitahara, Ryo

Citation: Kitazawa, Soichiro; Kameda, Tomoshi; Yagi-Utsumi, Maho; Sugase, Kenji; Baxter, Nicky; Kato, Koichi; Williamson, Mike; Kitahara, Ryo. "Solution Structure of the Q41N Variant of Ubiquitin as a Model for the Alternatively Folded N2 State of Ubiquitin"  Biochemistry 52, 1874-1885 (2013).

Assembly members:
entity, 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):
entity: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ NRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts344
15N chemical shifts79
1H chemical shifts566

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 76 residues - 8562.888 Da.

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

Samples:

sample_1: protein, [U-99% 13C; U-99% 15N], 2.0 mM; TRIS, [U-99% 2H], 20 mM; DSS 1 mM; H2O 93%; D2O 7%

sample_2: protein, [U-15N], 0.5 mM; TRIS, [U-99% 2H], 20 mM; DSS 1 mM; sodium chloride 250 mM; Pf1 bacteriopharge 6 ± 1 mg/mL; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

CYANA v3.93, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMRView v5.22, Johnson, One Moon Scientific - processing

NMR spectrometers:

  • Bruker DRX 600 MHz

Related Database Links:

BMRB 11547 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