BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17059

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

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:
STAM1, polymer, 178 residues, Formula weight is not available
ubiquitin, polymer, 156 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):
STAM1: PLFATNPFDQDVEKATSEMN TAEDWGLILDICDKVGQSRT GPKDCLRSIMRRVNHKDPHV AMQALTLLGACVSNCGKIFH LEVCSRDFASEVSNVLNKGH PKVCEKLKALMVEWTDEFKN DPQLSLISAMIKNLKEQGVT FPAIGSQAAEQAKASPALVA KDPGTVANKKEEEDLAKA
ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGAKKR KKKSYTTPKKNKHKRKKVKL AVLKYYKVDENGKISRLRRE CPSDECGAGVFMASHFDRHY CGKCCLTYCFNKPEDK

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
1STAM11
2ubiquitin2

Entities:

Entity 1, STAM1 178 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   ILELYSASNLEULYSGLUGLNGLYVALTHR
15   PHEPROALAILEGLYSERGLNALAALAGLU
16   GLNALALYSALASERPROALALEUVALALA
17   LYSASPPROGLYTHRVALALAASNLYSLYS
18   GLUGLUGLUASPLEUALALYSALA

Entity 2, ubiquitin 156 residues - Formula weight is not available

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLYALALYSLYSARG
9   LYSLYSLYSSERTYRTHRTHRPROLYSLYS
10   ASNLYSHISLYSARGLYSLYSVALLYSLEU
11   ALAVALLEULYSTYRTYRLYSVALASPGLU
12   ASNGLYLYSILESERARGLEUARGARGGLU
13   CYSPROSERASPGLUCYSGLYALAGLYVAL
14   PHEMETALASERHISPHEASPARGHISTYR
15   CYSGLYLYSCYSCYSLEUTHRTYRCYSPHE
16   ASNLYSPROGLUASPLYS

Samples:

sample_1: STAM1, [U-15N], 0.1 mM; ubiquitin, [U-15N], 0.02 – 0.5 mM; sodium phosphate 20 mM; DTT 1 mM; sodium chloride 0.1 M; PMSF 0.5 mM; sodium azide 0.05 mM; H2O 95%; D2O 5%

sample_2: STAM10.01 – 0.2 mM; ubiquitin, [U-15N], 0.05 mM; sodium phosphate 20 mM; DTT 1 mM; sodium chloride 0.1 M; PMSF 0.5 mM; sodium azide 0.05 mM; 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, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

KaleidaGraph v3.5, Synergy Software - data analysis

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker Avance 600 MHz

Related Database Links:

BMRB 16763 17065
PDB
DBJ BAE26170 BAE28168 BAE34187 BAE37536 BAE40949 BAA04129 BAA09096 BAA11843 BAB27296 BAB31357
GB AAC50734 AAC52840 AAH30586 AAH44666 AAH55326 AAA28997 AAA36788 AAA53067 AAA57047 AAB03872
REF NP_001070310 NP_001102591 NP_003464 NP_035614 XP_001094352 NP_001013290 NP_001016172 NP_001029037 NP_001086065 NP_001129064
SP P70297 Q92783 P0CG50 P0CG69 P62978 P62979 P62982
TPG DAA23567 DAA24675
EMBL CAA44911 CAA57432 CAG12343 CAI73380 CAJ83451
PIR UQHUR7