BMRB Entry 18737

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18737
MolProbity Validation Chart

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Title:
DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: M DETERMINANTS AND FUNCTIONAL IMPLICATIONS
Deposition date:
2012-09-24
Original release date:
2013-09-30
Authors:
Ortega-Roldan, J.; Azuaga, A.; Blackledge, M.; Van Nuland, N.
Citation:

Citation: Ortega-Roldan, Jose; Casares, Salvador; Ringkjobing-Jensen, Malene; Cardenes, Nayra; Bravo, Jeronimo; Blackledge, Martin; Azuaga, Ana; Van Nuland, Nico. "Distinct Ubiquitin Binding Modes Exhibited by SH3 domains. Molecular Determinants and Functional Implications"  PLoS One 8, e73018-e73018 (2013).
PubMed: 24039852

Assembly members:

Assembly members:
UBIQUITIN, polymer, 76 residues, 8576.914 Da.
CD2-ASSOCIATED_PROTEIN, polymer, 63 residues, 6830.602 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: ESCHERICHIA COLI   Vector: PET29B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UBIQUITIN: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG
CD2-ASSOCIATED_PROTEIN: AMGAKEYCRTLFPYTGTNED ELTFREGEIIHLISKETGEA GWWKGELNGKEGVFPDNFAV QIS

Data sets:
Data typeCount
15N chemical shifts133
1H chemical shifts133

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1UBIQUITIN1
2CD2-ASSOCIATED PROTEIN2

Entities:

Entity 1, UBIQUITIN 76 residues - 8576.914 Da.

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

Entity 2, CD2-ASSOCIATED PROTEIN 63 residues - 6830.602 Da.

1   ALAMETGLYALALYSGLUTYRCYSARGTHR
2   LEUPHEPROTYRTHRGLYTHRASNGLUASP
3   GLULEUTHRPHEARGGLUGLYGLUILEILE
4   HISLEUILESERLYSGLUTHRGLYGLUALA
5   GLYTRPTRPLYSGLYGLULEUASNGLYLYS
6   GLUGLYVALPHEPROASPASNPHEALAVAL
7   GLNILESER

Samples:

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

sample_2: Ubiquitin, [U-99% 15N], 0.25 mM; CD2AP SH3-C 1 mM; H2O 90%; D2O 10%

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

sample_4: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.828 mM; Ubiquitin, [U-99% 15N], 1.37 mM; H2O 90%; D2O 10%

sample_5: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.78 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O 10%

sample_6: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.25 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O 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, DOMINGUEZ, BOELENS - refinement, structure solution

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

NMRView, Johnson, One Moon Scientific - structure solution

NMR spectrometers:

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

Related Database Links:

BMRB 11505 11547 15047 15410 15689 15907 16228 16582 16626 16895 17181 17439 17769 17919 18582 18583 18584 18610 18611 19406 19412 25070 25123 25601 26604 4245 4375 15407 16643
PDB
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
GB AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
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
TPE CEL68433 CEL70397 CEL75964 CEL78064
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
AlphaFold P0C273 P0C275 P0C276 P0CG47 P0CG48

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks