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 17333

Title: Deubiquitinating function of ataxin-3: Insights from the solution structure of the Josephin domain   PubMed: 16118278

Authors: Mao, Yuxin; Senic-Matuglia, Francesca; Di Fiore, Pier; Polo, Simona; Hodsdon, Michael; De Camilli, Pietro

Citation: Mao, Yuxin; Senic-Matuglia, Francesca; Di Fiore, Pier Paolo; Polo, Simona; Hodsdon, Michael; De Camilli, Pietro. "Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain."  Proc. Natl. Acad. Sci. U.S.A. 102, 12700-12705 (2005).

Assembly members:
JD, polymer, 190 residues, Formula weight is not available
UB, polymer, 76 residues, Formula weight is not available

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):
JD: GPLGSMESIFHEKQEGSLCA QHCLNNLLQGEYFSPVELSS IAHQLDEEERMRMAEGGVTS EDYRTFLQQPSGNMDDSGFF SIQVISNALKVWGLELILFN SPEYQRLRIDPINERSFICN YKEHWFTVRKLGKQWFNLNS LLTGPELISDTYLALFLAQL QQEGYSIFVVKGDLPDCEAD QLLQMIRVQQ
UB: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
  • assigned_chemical_shifts
  • binding_constants
Data typeCount
binding constants4

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1JD1
2UB2

Entities:

Entity 1, JD 190 residues - Formula weight is not available

1   GLYPROLEUGLYSERMETGLUSERILEPHE
2   HISGLULYSGLNGLUGLYSERLEUCYSALA
3   GLNHISCYSLEUASNASNLEULEUGLNGLY
4   GLUTYRPHESERPROVALGLULEUSERSER
5   ILEALAHISGLNLEUASPGLUGLUGLUARG
6   METARGMETALAGLUGLYGLYVALTHRSER
7   GLUASPTYRARGTHRPHELEUGLNGLNPRO
8   SERGLYASNMETASPASPSERGLYPHEPHE
9   SERILEGLNVALILESERASNALALEULYS
10   VALTRPGLYLEUGLULEUILELEUPHEASN
11   SERPROGLUTYRGLNARGLEUARGILEASP
12   PROILEASNGLUARGSERPHEILECYSASN
13   TYRLYSGLUHISTRPPHETHRVALARGLYS
14   LEUGLYLYSGLNTRPPHEASNLEUASNSER
15   LEULEUTHRGLYPROGLULEUILESERASP
16   THRTYRLEUALALEUPHELEUALAGLNLEU
17   GLNGLNGLUGLYTYRSERILEPHEVALVAL
18   LYSGLYASPLEUPROASPCYSGLUALAASP
19   GLNLEULEUGLNMETILEARGVALGLNGLN

Entity 2, UB 76 residues - Formula weight is not available

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

Samples:

sample_1: azide 0.05%; 2,2-dimethyl-2-silapentane-5-sulfonate 10 uM; PMSF 1 uM; leupeptin 1 uM; pepstatin 1 uM; potassium phosphate 20 mM; JD, [U-15N], 100 uM; UB33 – 2400 uM; H2O 95%; D2O 5%

sample_2: azide 0.05%; 2,2-dimethyl-2-silapentane-5-sulfonate 10 uM; PMSF 1 uM; leupeptin 1 uM; pepstatin 1 uM; potassium phosphate 20 mM; JD, [U-15N, U-13C], 100 uM; UB33 – 2400 uM; H2O 95%; D2O 5%

sample_3: azide 0.05%; 2,2-dimethyl-2-silapentane-5-sulfonate 10 uM; PMSF 1 uM; leupeptin 1 uM; pepstatin 1 uM; potassium phosphate 20 mM; UB, [U-15N], uM; H2O 95%; D2O 5%

sample_4: azide 0.05%; 2,2-dimethyl-2-silapentane-5-sulfonate 10 uM; PMSF 1 uM; leupeptin 1 uM; pepstatin 1 uM; potassium phosphate 20 mM; UB, [U-15N], 33 – 2400 uM; JD 100 uM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - visual analysis

SIGMAPLOT, Systat Software, Inc., Point Richmond, CA - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAB18798 BAB25825 BAB55645 BAB55646 BAC27155 BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA72986 CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
GB AAB33571 AAB63352 AAB63353 AAB63354 AAH33711 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
REF NP_001092686 NP_001116553 NP_001124408 NP_001158250 NP_001161386 NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP O35815 P54252 Q9CVD2 P0C273 P0C275 P0C276 P0CG47 P0CG48
TPG DAA17354 DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
BMRB 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17239 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
TPD FAA00319