BMRB Entry 16813

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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/BMR16813
MolProbity Validation Chart

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Title:
Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain
Deposition date:
2010-03-31
Original release date:
2010-05-19
Authors:
Trempe, Jean-Francois; Guennadi, Kozlov; Edna, Camacho; Kalle, Gehring
Citation:

Citation: Trempe, Jean-Francois; Chen, Carol X-Q; Grenier, Karl; Camacho, Edna Matta; Kozlov, Guennadi; McPherson, Peter; Gehring, Kalle; Fon, Edward. "SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination."  Mol. Cell 36, 1034-1047 (2009).
PubMed: 20064468

Assembly members:

Assembly members:
Ubl, polymer, 81 residues, 8738.083 Da.
SH3, polymer, 71 residues, 7121.919 Da.

Natural source:

Natural source:   Common Name: Norway rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-6p1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubl: GPLGSMIVFVRFNSSYGFPV EVDSDTSIFQLKEVVAKRQG VPADQLRVIFAGKELQNHLT VQNCDLEQQSIVHIVQRPQR K
SH3: GSRRASVGSDQPCCRALYDF EPENEGELGFKEGDIITLTN QIDENWYEGMLHGQSGFFPI NYVEILVALPH

Data sets:
Data typeCount
13C chemical shifts406
15N chemical shifts150
1H chemical shifts833

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Ubl1
2SH32

Entities:

Entity 1, Ubl 81 residues - 8738.083 Da.

Residues 1-5 represent a non-native tag generated after 3C protease cleavage of N-terminal GST

1   GLYPROLEUGLYSERMETILEVALPHEVAL
2   ARGPHEASNSERSERTYRGLYPHEPROVAL
3   GLUVALASPSERASPTHRSERILEPHEGLN
4   LEULYSGLUVALVALALALYSARGGLNGLY
5   VALPROALAASPGLNLEUARGVALILEPHE
6   ALAGLYLYSGLULEUGLNASNHISLEUTHR
7   VALGLNASNCYSASPLEUGLUGLNGLNSER
8   ILEVALHISILEVALGLNARGPROGLNARG
9   LYS

Entity 2, SH3 71 residues - 7121.919 Da.

Residues 1-9 represent a non-native tag generated after thrombin protease cleavage of N-terminal GST

1   GLYSERARGARGALASERVALGLYSERASP
2   GLNPROCYSCYSARGALALEUTYRASPPHE
3   GLUPROGLUASNGLUGLYGLULEUGLYPHE
4   LYSGLUGLYASPILEILETHRLEUTHRASN
5   GLNILEASPGLUASNTRPTYRGLUGLYMET
6   LEUHISGLYGLNSERGLYPHEPHEPROILE
7   ASNTYRVALGLUILELEUVALALALEUPRO
8   HIS

Samples:

Ubl_SH3_D2O: Ubl, [U-99% 13C; U-99% 15N], 1.2 ± 0.1 mM; SH3 1.2 ± 0.1 mM; D2O 100%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_D2O: SH3, [U-99% 13C; U-99% 15N], 1.2 mM; Ubl 1.2 mM; D2O 100%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

Ubl_SH3_H2O: Ubl, [U-99% 13C; U-99% 15N], 0.8 mM; SH3 1.6 mM; D2O 5%; H2O 95%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_H2O: SH3, [U-99% 13C; U-99% 15N], 0.8 mM; Ubl 1.6 mM; D2O 5%; H2O 95%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

Ubl_SH3_H2OB: Ubl, [U-99% 15N], 0.8 mM; SH3 1.6 mM; D2O 5%; H2O 95%; polyacrylamide 4.5%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_H2OB: SH3, [U-99% 15N], 0.8 mM; Ubl 1.6 mM; D2O 5%; H2O 95%; polyacrylamide 4.5%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

isotropic: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

polyacrylamide: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
3D CBCA(CO)NHUbl_SH3_H2Oisotropicisotropic
3D HNCACBUbl_SH3_H2Oisotropicisotropic
3D CBCA(CO)NHSH3_Ubl_H2Oisotropicisotropic
3D HNCACBSH3_Ubl_H2Oisotropicisotropic
2D 1H-15N HSQCUbl_SH3_H2Oisotropicisotropic
2D 1H-15N HSQCSH3_Ubl_H2Oisotropicisotropic
3D HCCH-COSYUbl_SH3_D2Oisotropicisotropic
3D HCCH-COSYSH3_Ubl_D2Oisotropicisotropic
3D 1H-13C NOESYUbl_SH3_D2Oisotropicisotropic
3D 1H-13C NOESYSH3_Ubl_D2Oisotropicisotropic
2D 1H-13C HSQCUbl_SH3_D2Oisotropicisotropic
2D 1H-13C HSQCSH3_Ubl_D2Oisotropicisotropic
2D 1H-15N IPAP-HSQCUbl_SH3_H2OBanisotropicpolyacrylamide
2D 1H-15N IPAP-HSQCSH3_Ubl_H2OBanisotropicpolyacrylamide
2D 1H-15N IPAP-HSQCUbl_SH3_H2OBisotropicisotropic
2D 1H-15N IPAP-HSQCSH3_Ubl_H2OBisotropicisotropic
3D 1H-13C NOESY coupledUbl_SH3_D2Oisotropicisotropic
3D 1H-13C NOESY coupledSH3_Ubl_D2Oisotropicisotropic

Software:

NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.115, Goddard - chemical shift assignment, peak picking

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Varian INOVA 800 MHz

Related Database Links:

PDB
DBJ BAA92431 BAC31888 BAE22364 BAE23963
GB AAF34874 AAF68666 AAG37013 AAM21453 AAM21456 AAH18385 AAI23533 AAL37407 AAL37408 AIL95726
REF NP_064478 NP_001070308 NP_062408 XP_001925192 XP_002920770 XP_003783082
SP Q9JK66 Q62420
TPG DAA26952
AlphaFold Q9JK66 Q62420

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