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 16763

Title: Identification of a novel ubiquitin binding site of STAM1 VHS domain by NMR spectroscopy   PubMed: 19111546

Authors: Hong, Yoon-Hun; Ahn, Hee-Chul; Lim, Jongsoo; Kim, Hong-Man; Ji, Hye-Young; Lee, Seunga; Kim, Ji-Hun; Park, Eun; Song, Hyun; Lee, Bong-Jin

Citation: Hong, Yoon-Hun; Ahn, Hee-Chul; Lim, Jongsoo; Kim, Hong-Man; Ji, Hye-Young; Lee, Seunga; Kim, Ji-Hun; Park, Eun; Song, Hyun; Lee, Bong-Jin. "Identification of a novel ubiquitin binding site of STAM1 VHS domain by NMR spectroscopy"  FEBS Lett. 583, 287-292 (2009).

Assembly members:
VHS, polymer, 138 residues, Formula weight is not available
ubiquitin, 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):
VHS: PLFATNPFDQDVEKATSEMN TAEDWGLILDICDKVGQSRT GPKDCLRSIMRRVNHKDPHV AMQALTLLGACVSNCGKIFH LEVCSRDFASEVSNVLNKGH PKVCEKLKALMVEWTDEFKN DPQLSLISAMIKNLKEQG
ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
  • assigned_chemical_shifts
  • binding_constants
Data typeCount
binding constants2

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1VHS1
2ubiquitin2

Entities:

Entity 1, VHS 138 residues - Formula weight is not available

1   PROLEUPHEALATHRASNPROPHEASPGLN
2   ASPVALGLULYSALATHRSERGLUMETASN
3   THRALAGLUASPTRPGLYLEUILELEUASP
4   ILECYSASPLYSVALGLYGLNSERARGTHR
5   GLYPROLYSASPCYSLEUARGSERILEMET
6   ARGARGVALASNHISLYSASPPROHISVAL
7   ALAMETGLNALALEUTHRLEULEUGLYALA
8   CYSVALSERASNCYSGLYLYSILEPHEHIS
9   LEUGLUVALCYSSERARGASPPHEALASER
10   GLUVALSERASNVALLEUASNLYSGLYHIS
11   PROLYSVALCYSGLULYSLEULYSALALEU
12   METVALGLUTRPTHRASPGLUPHELYSASN
13   ASPPROGLNLEUSERLEUILESERALAMET
14   ILELYSASNLEULYSGLUGLNGLY

Entity 2, ubiquitin 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: VHS, [U-100% 15N], 0.1 mM; ubiquitin0.02 – 0.5 mM; sodium phosphate buffer 20 mM; DTT 1 mM; sodium chloride 0.1 mM; PMSF 0.5 mM; sodium azide 0.05%; H2O 95%; D2O 5%

sample_2: VHS 0.0.01-0.2 mM; ubiquitin, [U-100% 15N], 0.05 mM; sodium phosphate buffer 20 mM; DTT 1 mM; sodium chloride 0.1 mM; PMSF 0.5 mM; sodium azide 0.05%; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

KaleidaGraph v3.5, Synergy Software - non-linear regression

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker Avance 600 MHz
  • Varian VNMRS 900 MHz

Related Database Links:

BMRB 17059 17065 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16880 16885 16895 17059 17181 17239 17333 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
PDB
DBJ BAE26170 BAE28168 BAE34187 BAE37536 BAE40949 BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
GB AAC50734 AAC52840 AAH30586 AAH44666 AAH55326 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
REF NP_001070310 NP_001102591 NP_003464 NP_035614 XP_001094352 NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P70297 Q92783 P0C273 P0C275 P0C276 P0CG47 P0CG48
TPG DAA23567 DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
EMBL CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
TPD FAA00319