BMRB Entry 11569

Title:
Chemical Shift Assignments for MIP and MDM2 in bound state
Deposition date:
2014-06-03
Original release date:
2015-06-02
Authors:
Nagata, Takashi; Shirakawa, Kie; Kobayashi, Naohiro; Shiheido, Hidekazu; Horisawa, Kenichi; Katahira, Masato; Doi, Nobuhide; Yanagawa, Hiroshi
Citation:

Citation: Nagata, Takashi; Shirakawa, Kie; Kobayashi, Naohiro; Shiheido, Hidekazu; Horisawa, Kenichi; Katahira, Masato; Doi, Nobuhide; Yanagawa, Hiroshi. "Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display"  Plos One 9, e109163-e109163 (2014).
PubMed: 25275651

Assembly members:

Assembly members:
MIP-MDM2, polymer, 131 residues, 15031.517 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

Data sets:
Data typeCount
13C chemical shifts575
15N chemical shifts115
1H chemical shifts863

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 131 residues - 15031.517 Da.

Residues -11Met to 1Glu corresponds to 0Met to 12Glu of MIP peptide, residues 2Gly to 10Gln represents TEV cleavage sequence, residues 11Gly to 108Met corresponds to MDM2, and residues M109 to 119Gly represents T7tag."

1   METPROARGPHETRPGLUTYRTRPLEUARG
2   LEUMETGLUGLYGLYGLYGLUASNLEUTYR
3   PHEGLNGLYMETSERVALPROTHRASPGLY
4   ALAVALTHRTHRSERGLNILEPROALASER
5   GLUGLNGLUTHRLEUVALARGPROLYSPRO
6   LEULEULEULYSLEULEULYSSERVALGLY
7   ALAGLNLYSASPTHRTYRTHRMETLYSGLU
8   VALLEUPHETYRLEUGLYGLNTYRILEMET
9   THRLYSARGLEUTYRASPGLULYSGLNGLN
10   HISILEVALTYRCYSSERASNASPLEULEU
11   GLYASPLEUPHEGLYVALPROSERPHESER
12   VALLYSGLUHISARGLYSILETYRTHRMET
13   METALASERMETTHRGLYGLYGLNGLNMET
14   GLY

Samples:

sample_1: MIP-MDM2 fusion, [U-100% 13C; U-100% 15N], 300 uM; TRIS 20 mM; sodium chloride 300 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 160 mM; pH: 7.6; 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 CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1

Software:

AMBER v12, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v2.0.14, Guntert, Mumenthaler and Wuthrich - structure solution

Kujira v0.984, Naohiro Kobayashi - chemical shift assignment

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

CHIMERA, UCSF - data analysis

NMR spectrometers:

  • Bruker DRX 600 MHz

Related Database Links:

BMRB 18755 18876 2410
PDB
DBJ BAF83030 BAJ17752
EMBL CAA78055 CAD23251 CAD36959 CAH89564 CAP16708
GB AAA60568 AAI48523 AAI52385 AAI52391 AAI53118
PRF 1814460A
REF NP_001124685 NP_001138809 NP_001138811 NP_001253331 NP_002383
SP Q00987
AlphaFold Q00987

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