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 28042

Title: ubiquitin receptor protein complex   PubMed: 32160516

Deposition date: 2019-11-13 Original release date: 2020-03-03

Authors: Lu, Xiuxiu; Walters, Kylie

Citation: Lu, Xiuxiu; Ebelle, Danielle; Matsuo, Hiroshi; Walters, Kylie. "An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure"  Structure 28, 495-506.e3 (2020).

Assembly members:
ubiquitin_receptor_A, polymer, 136 residues, Formula weight is not available
ubiquitin_receptor_B, polymer, 36 residues, Formula weight is not available
ubiquitin_receptor_C, polymer, 77 residues, Formula weight is not available
ubiquitin_receptor_D, 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):
ubiquitin_receptor_A: GPGSMTTSGALFPSLVPGSR GASNKYLVEFRAGKMSLKGT TVTPDKRKGLVYIQQTDDSL IHFCWKDRTSGNVEDDLIIF PDDCEFKRVPQCPSGRVYVL KFKAGSKRLFFWMQEPKTDQ DEEHCRKVNEYLNNPP
ubiquitin_receptor_B: MPGALGASGSSGHELSALGP GSQEPEPPEPFEYIDD
ubiquitin_receptor_C: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGD
ubiquitin_receptor_D: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGRQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data typeCount
13C chemical shifts1165
15N chemical shifts207
1H chemical shifts1930

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ubiquitin receptor, chain A1
2ubiquitin receptor, chain B2
3ubiquitin receptor, chain C3
4ubiquitin receptor, chain D4

Entities:

Entity 1, ubiquitin receptor, chain A 136 residues - Formula weight is not available

1   GLYPROGLYSERMETTHRTHRSERGLYALA
2   LEUPHEPROSERLEUVALPROGLYSERARG
3   GLYALASERASNLYSTYRLEUVALGLUPHE
4   ARGALAGLYLYSMETSERLEULYSGLYTHR
5   THRVALTHRPROASPLYSARGLYSGLYLEU
6   VALTYRILEGLNGLNTHRASPASPSERLEU
7   ILEHISPHECYSTRPLYSASPARGTHRSER
8   GLYASNVALGLUASPASPLEUILEILEPHE
9   PROASPASPCYSGLUPHELYSARGVALPRO
10   GLNCYSPROSERGLYARGVALTYRVALLEU
11   LYSPHELYSALAGLYSERLYSARGLEUPHE
12   PHETRPMETGLNGLUPROLYSTHRASPGLN
13   ASPGLUGLUHISCYSARGLYSVALASNGLU
14   TYRLEUASNASNPROPRO

Entity 2, ubiquitin receptor, chain B 36 residues - Formula weight is not available

1   METPROGLYALALEUGLYALASERGLYSER
2   SERGLYHISGLULEUSERALALEUGLYPRO
3   GLYSERGLNGLUPROGLUPROPROGLUPRO
4   PHEGLUTYRILEASPASP

Entity 3, ubiquitin receptor, chain C 77 residues - Formula weight is not available

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

Entity 4, ubiquitin receptor, chain D 76 residues - Formula weight is not available

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

Samples:

sample_1: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM

sample_2: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM

sample_conditions_1: ionic strength: 0.11 M; pH: 6.5; pressure: 1 atm; temperature: 298.15 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D half-filtered 1H-13C NOESYsample_1isotropicsample_conditions_1
3D half-filtered 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

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

XEASY, Bartels et al. - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Bruker Avance 850 MHz
  • Bruker Avance 900 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts