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 25709

Title: Methyl resonances of ubiquitin S65E in complex with R0RBR domain (141-465) of parkin   PubMed: 26254304

Deposition date: 2015-07-14 Original release date: 2015-08-14

Authors: Shaw, Gary; Condos, Tara

Citation: Kumar, Atul; Aguirre, Jacob; Condos, Tara; Martinez-Torres, R. Julio; Chaugule, Viduth; Toth, Rachel; Sundaramoorthy, Ramasubramanian; Mercier, Pascal; Knebel, Axel; Spratt, Donald; Barber, Kathryn; Shaw, Gary; Walden, Helen. "Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis"  EMBO J. 34, 2506-2521 (2015).

Assembly members:
Ub_S65E, polymer, 79 residues, Formula weight is not available
Parkin_R0RBR_(141-465), polymer, 325 residues, Formula weight is not available
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Ub_S65E: SNAMQIFVKTLTGKTITLEV ESSDTIDNVKSKIQDKEGIP PDQQRLIFAGKQLEDGRTLS DYNIQKEETLHLVLRLRGG
Parkin_R0RBR_(141-465): SIYNSFYVYCKGPCQRVQPG KLRVQCSTCRQATLTLTQGP SCWDDVLIPNRMSGECQSPH CPGTSAEFFFKCGAHPTSDK ETSVALHLIATNSRNITCIT CTDVRSPVLVFQCNSRHVIC LDCFHLYCVTRLNDRQFVHD PQLGYSLPCVAGCPNSLIKE LHHFRILGEEQYNRYQQYGA EECVLQMGGVLCPRPGCGAG LLPEPDQRKVTCEGGNGLGC GFAFCRECKEAYHEGECSAV FEASGTTTQAYRVDERAAEQ ARWEAASKETIKKTTKPCPR CHVPVEKNGGCMHMKCPQPQ CRLEWCWNCGCEWNRVCMGD HWFDV

Data sets:
Data typeCount
13C chemical shifts38
1H chemical shifts114

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Ub S65E1
2parkin R0RBR2
3ZINC ION 13
4ZINC ION 23
5ZINC ION 33
6ZINC ION 43
7ZINC ION 53
8ZINC ION 63
9ZINC ION 73
10ZINC ION 83

Entities:

Entity 1, Ub S65E 79 residues - Formula weight is not available

1   SERASNALAMETGLNILEPHEVALLYSTHR
2   LEUTHRGLYLYSTHRILETHRLEUGLUVAL
3   GLUSERSERASPTHRILEASPASNVALLYS
4   SERLYSILEGLNASPLYSGLUGLYILEPRO
5   PROASPGLNGLNARGLEUILEPHEALAGLY
6   LYSGLNLEUGLUASPGLYARGTHRLEUSER
7   ASPTYRASNILEGLNLYSGLUGLUTHRLEU
8   HISLEUVALLEUARGLEUARGGLYGLY

Entity 2, parkin R0RBR 325 residues - Formula weight is not available

1   SERILETYRASNSERPHETYRVALTYRCYS
2   LYSGLYPROCYSGLNARGVALGLNPROGLY
3   LYSLEUARGVALGLNCYSSERTHRCYSARG
4   GLNALATHRLEUTHRLEUTHRGLNGLYPRO
5   SERCYSTRPASPASPVALLEUILEPROASN
6   ARGMETSERGLYGLUCYSGLNSERPROHIS
7   CYSPROGLYTHRSERALAGLUPHEPHEPHE
8   LYSCYSGLYALAHISPROTHRSERASPLYS
9   GLUTHRSERVALALALEUHISLEUILEALA
10   THRASNSERARGASNILETHRCYSILETHR
11   CYSTHRASPVALARGSERPROVALLEUVAL
12   PHEGLNCYSASNSERARGHISVALILECYS
13   LEUASPCYSPHEHISLEUTYRCYSVALTHR
14   ARGLEUASNASPARGGLNPHEVALHISASP
15   PROGLNLEUGLYTYRSERLEUPROCYSVAL
16   ALAGLYCYSPROASNSERLEUILELYSGLU
17   LEUHISHISPHEARGILELEUGLYGLUGLU
18   GLNTYRASNARGTYRGLNGLNTYRGLYALA
19   GLUGLUCYSVALLEUGLNMETGLYGLYVAL
20   LEUCYSPROARGPROGLYCYSGLYALAGLY
21   LEULEUPROGLUPROASPGLNARGLYSVAL
22   THRCYSGLUGLYGLYASNGLYLEUGLYCYS
23   GLYPHEALAPHECYSARGGLUCYSLYSGLU
24   ALATYRHISGLUGLYGLUCYSSERALAVAL
25   PHEGLUALASERGLYTHRTHRTHRGLNALA
26   TYRARGVALASPGLUARGALAALAGLUGLN
27   ALAARGTRPGLUALAALASERLYSGLUTHR
28   ILELYSLYSTHRTHRLYSPROCYSPROARG
29   CYSHISVALPROVALGLULYSASNGLYGLY
30   CYSMETHISMETLYSCYSPROGLNPROGLN
31   CYSARGLEUGLUTRPCYSTRPASNCYSGLY
32   CYSGLUTRPASNARGVALCYSMETGLYASP
33   HISTRPPHEASPVAL

Entity 3, ZINC ION 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Ub S65E, [U-99% 13C; U-99% 15N], 290 uM; Parkin R0RBR (141-465), [U-99% 2H], 290 uM; HEPES 25 mM; Sodium chloride 100 mM; TCEP 500 uM; Imidazole 500 uM; DSS 100 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HMQC aliphaticsample_1isotropicsample_conditions_1

Software:

NMRView v8.2.36, Johnson, One Moon Scientific - chemical shift assignment, peak picking

VNMRJ v3.2, Varian - collection

NMRPipe v2010.260.15.01, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz