BMRB Entry 30197

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30197
MolProbity Validation Chart

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Title:
Solution structure of Serine 65 phosphorylated UBL domain from parkin
Deposition date:
2016-10-25
Original release date:
2016-12-15
Authors:
Aguirre, J.; Dunkerley, K.; Mercier, P.; Shaw, G.
Citation:

Citation: Aguirre, J.; Dunkerley, K.; Mercier, P.; Shaw, G.. "Structure of phosphorylated parkin UBL domain and insights into PINK1-orchestrated activation"  Proc. Natl. Acad. Sci. U.S.A. 114, 298-303 (2017).
PubMed: 28007983

Assembly members:

Assembly members:
E3 ubiquitin-protein ligase parkin, polymer, 76 residues, 8916.063 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET SUMO

Entity Sequences (FASTA):

Entity Sequences (FASTA):
E3 ubiquitin-protein ligase parkin: MIVFVRFNSSHGFPVEVDSD TSIFQLKEVVAKRQGVPADQ LRVIFAGKELRNDWTVQNCD LDQQXIVHIVQRPWRK

Data sets:
Data typeCount
13C chemical shifts335
15N chemical shifts80
1H chemical shifts502

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 76 residues - 8916.063 Da.

1   METILEVALPHEVALARGPHEASNSERSER
2   HISGLYPHEPROVALGLUVALASPSERASP
3   THRSERILEPHEGLNLEULYSGLUVALVAL
4   ALALYSARGGLNGLYVALPROALAASPGLN
5   LEUARGVALILEPHEALAGLYLYSGLULEU
6   ARGASNASPTRPTHRVALGLNASNCYSASP
7   LEUASPGLNGLNSEPILEVALHISILEVAL
8   GLNARGPROTRPARGLYS

Samples:

sample_2: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-15N], 300 uM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_3: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-13C], 300 uM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_4: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-99% 13C; U-99% 15N], 400 uM; sodium chloride 100 mM; H2O 90%; D2O 10%

sample_5: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL 400 uM; sodium chloride 100 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_5isotropicsample_conditions_1
3D HNCAsample_4isotropicsample_conditions_1
3D HNCACBsample_4isotropicsample_conditions_1
3D HNCOsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_5isotropicsample_conditions_1
3D C(CO)NHsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_5isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe v8.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.2.4, Johnson, One Moon Scientific - data analysis

VNMR v3.2, Varian - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks