BMRB Entry 11040

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11040
MolProbity Validation Chart

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Title:
Structural Basis of PxxDY motif recognition in SH3 binding
Deposition date:
2008-04-02
Original release date:
2008-08-28
Authors:
Aitio, Olli; Hellman, Maarit; Kesti, Tapio; Kleino, Iivari; Sumoilova, Olga; Tossavainen, Helena; Paakkonen, Kimmo; Saksela, Kalle; Permi, Perttu
Citation:

Citation: Aitio, Olli; Hellman, Maarit; Kesti, Tapio; Kleino, Iivari; Samuilova, Olga; Paakkonen, Kimmo; Tossavainen, Helena; Saksela, Kalle; Permi, Perttu. "Structural basis of PxxDY motif recognition in SH3 binding"  J. Mol. Biol. 382, 167-178 (2008).
PubMed: 18644376

Assembly members:

Assembly members:
Eps8L1SH3, polymer, 64 residues, 7301.219 Da.
CD3e peptide, polymer, 12 residues, 1394.566 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Eps8L1SH3: GSMGTAGKWVLCNYDFQARN SSELSVKQRDVLEVLDDSRK WWKVRDPAGQEGYVPYNILT PYPG
CD3e peptide: PPVPNPDYEPIR

Data sets:
Data typeCount
13C chemical shifts225
15N chemical shifts62
1H chemical shifts509

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Eps8L1SH31
2CD3e peptide2

Entities:

Entity 1, Eps8L1SH3 64 residues - 7301.219 Da.

1   GLYSERMETGLYTHRALAGLYLYSTRPVAL
2   LEUCYSASNTYRASPPHEGLNALAARGASN
3   SERSERGLULEUSERVALLYSGLNARGASP
4   VALLEUGLUVALLEUASPASPSERARGLYS
5   TRPTRPLYSVALARGASPPROALAGLYGLN
6   GLUGLYTYRVALPROTYRASNILELEUTHR
7   PROTYRPROGLY

Entity 2, CD3e peptide 12 residues - 1394.566 Da.

1   PROPROVALPROASNPROASPTYRGLUPRO
2   ILEARG

Samples:

sample_1: Eps8L1SH3, [U-98% 13C; U-98% 15N], 0.8 mM; CD3e peptide 2.4 mM; Tris-HCl 10 mM; NaCl 50 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D iHNCACBsample_1isotropicsample_conditions_1
3D iHNCAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D CC(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 13C,15N-filteded/15N-edited NOESYsample_1isotropicsample_conditions_1
3D 13C,15N-filtered/13C-edited NOESYsample_1isotropicsample_conditions_1
2D 13C/15N -filtered TOCSYsample_1isotropicsample_conditions_1
2D 13C/15N -filtered NOESYsample_1isotropicsample_conditions_1

Software:

CYANA v2.0, P.GUNTERT ET AL. - structure solution

AMBER v8.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

VNMR, Varian - collection, processing

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAA91041 BAC11399 BAG51855 BAG59319 BAG63100
GB AAG03038 AAG03039 AAH15763 AAL76117 AAQ15231
REF NP_060199 NP_573441 XP_003809943 XP_003809945 XP_003953676
SP Q8TE68
AlphaFold Q8TE68 A8K997

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