BMRB Entry 15074

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15074
MolProbity Validation Chart

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Title:
Assignment of the 1H, 15N and 13C resonances and determination of the 3D- structure of In-Between-RING (IBR) domain of Parkin
Deposition date:
2006-12-12
Original release date:
2007-05-09
Authors:
Shaw, Gary; Beasley, Steven
Citation:

Citation: Beasley, Steven; Hristova, Ventzislava; Shaw, Gary. "Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson's disease."  Proc. Natl. Acad. Sci. U. S. A. 104, 3095-3100 (2007).
PubMed: 17360614

Assembly members:

Assembly members:
IBR_domain_of_human_Parkin, polymer, 80 residues, 8610.6 Da.
ZN, non-polymer, 65.409 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: p11 (modified pET15b)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IBR_domain_of_human_Parkin: GHMGEEQYNRYQQYGAEECV LQMGGVLCPRPGCGAGLLPE PDQRKVTCEGGNGLGCGFAF CRECKEAYHEGECSAVFEAS

Data sets:
Data typeCount
13C chemical shifts289
15N chemical shifts81
1H chemical shifts475

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1IBR domain of Parkin1
2zinc ion, 12
3zinc ion, 22

Entities:

Entity 1, IBR domain of Parkin 80 residues - 8610.6 Da.

Residues 1-2 are artifacts of a non-native affinity tag

1   GLYHISMETGLYGLUGLUGLNTYRASNARG
2   TYRGLNGLNTYRGLYALAGLUGLUCYSVAL
3   LEUGLNMETGLYGLYVALLEUCYSPROARG
4   PROGLYCYSGLYALAGLYLEULEUPROGLU
5   PROASPGLNARGLYSVALTHRCYSGLUGLY
6   GLYASNGLYLEUGLYCYSGLYPHEALAPHE
7   CYSARGGLUCYSLYSGLUALATYRHISGLU
8   GLYGLUCYSSERALAVALPHEGLUALASER

Entity 2, zinc ion, 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: IBR, [U-100% 13C; U-100% 15N], 0.2 mM; sodium phosphate, none, 25 mM; sodium chloride, none, 100 mM; DTT, none, 1 mM; DSS, none, 0.033 mM

sample_2: IBR, [U-100% 13C; U-100% 15N], 0.2 mM; sodium phosphate, none, 25 mM; sodium chloride, none, 100 mM; DTT, none, 1 mM; DSS, none, 0.033 mM

sample_conditions_1: ionic strength: 125 mM; pH: 6.95; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HC(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HBCBCHCDHDsample_2isotropicsample_conditions_1
2D NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

CYANA v2.5.4, P Guntert, C Mumenthaler and K Wuthrich - structure solution

NMRView v5.0.4.sol7, B Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

NMRPipe v2.3, F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAA25751 BAF43729 BAF85279 BAG57845 BAI46122
EMBL CAH90914
GB AAM21457 AAM21459 AAM21461 AAS88422 ADB90270
REF NP_001125521 NP_004553 NP_054642 NP_054643 XP_001099588
SP O60260
AlphaFold O60260

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