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 19447

Title: DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: MOLECULAR DETERMINANTS AND FUNCTIONAL IMPLICATIONS   PubMed: 24039852

Authors: Ortega-Roldan, J.; Salmon, L.; Azuaga, A.; Blackledge, M.; Van Nuland, N.

Citation: Ortega-Roldan, J.; Casares, S.; Ringkjobing-Jensen, M.; Cardenes, N.; Bravo, N.; Blackledge, M.; Azuaga, A.; Van Nuland, N.. "Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications"  PLoS One 8, e73018-e73018 (2013).

Assembly members:
SH3A, polymer, 61 residues, 6764.630 Da.
Ubiquitin, polymer, 76 residues, 8576.914 Da.

Natural source:   Common Name: house mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

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

Entity Sequences (FASTA):
SH3A: VDYIVEYDYDAVHDDELTIR VGEIIRNVKKLQEEGWLEGE LNGRRGMFPDNFVKEIKRET E
Ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
15N chemical shifts132
1H chemical shifts132

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SH3A1
2Ubiquitin2

Entities:

Entity 1, SH3A 61 residues - 6764.630 Da.

1   VALASPTYRILEVALGLUTYRASPTYRASP
2   ALAVALHISASPASPGLULEUTHRILEARG
3   VALGLYGLUILEILEARGASNVALLYSLYS
4   LEUGLNGLUGLUGLYTRPLEUGLUGLYGLU
5   LEUASNGLYARGARGGLYMETPHEPROASP
6   ASNPHEVALLYSGLUILELYSARGGLUTHR
7   GLU

Entity 2, Ubiquitin 76 residues - 8576.914 Da.

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

Samples:

sample_1: CD2AP SH3-A, [U-99% 15N], 0.2 mM; Ubiquitin 1 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: CD2AP SH3-A mM; Ubiquitin, [U-99% 15N], 0.25 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_3: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.9 mM; Ubiquitin, [U-99% 15N], 0.46 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_4: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.8 mM; Ubiquitin, [U-99% 15N], 1.37 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_5: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.7 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_6: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.25 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCO JNH, JCC, JCH, JCAHAsample_3anisotropicsample_conditions_1
3D HNCO JNH, JCC, JCH, JCAHAsample_4anisotropicsample_conditions_1
3D HNCO JNH, JCC, JCH, JCAHAsample_5anisotropicsample_conditions_1
2D 1H-15N HSQC FILTERED DIPSAPsample_6anisotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

HADDOCK vCNS/SCULPTOR, DOMINGUEZ, BOELENS - refinement

CNS/SCULPTOR, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMRView, Johnson, One Moon Scientific - structure solution

HADDOCK, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • VARIAN UNIFORM NMR SYSTEM 600 MHz
  • Varian Uniform NMR System 800 MHz

Related Database Links:

BMRB 16641 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
PDB
GB ELW65647 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
REF NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P0C273 P0C275 P0C276 P0CG47 P0CG48
TPD FAA00319
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295