BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19230

Title: Solution structure of Hdm2 with engineered cyclotide   PubMed: 23848581

Authors: Majumder, Subhabrata; Ji, Yanbin; Millard, Melissa; Borra, Radikha; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Camarero, Julio

Citation: Ji, Yanbin; Majumder, Subhabrata; Millard, Melissa; Borra, Radhika; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Shekhtman, Alexander; Camarero, Julio. "In Vivo Activation of the p53 Tumor Suppressor Pathway by an Engineered Cyclotide."  J. Am. Chem. Soc. 135, 11623-11633 (2013).

Assembly members:
Hdm2, polymer, 51 residues, 5291.016 Da.
MCo-PMI, polymer, 83 residues, 9814.753 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Hdm2: SGSGASKAPTSFAEYWNLLS AGGVCPKILQRCRRDSDCPG ACICRGNGYCG
MCo-PMI: LVRPKPLLLKLLKSVGAQKD TYTMKEVLFYLGQYIMTKRL YDEKQQHIVYCSNDLLGDLF GVPSFSVKEHRKIYTMIYRN LVV

Data sets:
Data typeCount
13C chemical shifts147
15N chemical shifts121
1H chemical shifts581

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Hdm21
2MCo-PMI2

Entities:

Entity 1, Hdm2 51 residues - 5291.016 Da.

This is an engineered cyclotide based on MCoTI-I., cyclic-pseudo-peptide

1   SERGLYSERGLYALASERLYSALAPROTHR
2   SERPHEALAGLUTYRTRPASNLEULEUSER
3   ALAGLYGLYVALCYSPROLYSILELEUGLN
4   ARGCYSARGARGASPSERASPCYSPROGLY
5   ALACYSILECYSARGGLYASNGLYTYRCYS
6   GLY

Entity 2, MCo-PMI 83 residues - 9814.753 Da.

1   LEUVALARGPROLYSPROLEULEULEULYS
2   LEULEULYSSERVALGLYALAGLNLYSASP
3   THRTYRTHRMETLYSGLUVALLEUPHETYR
4   LEUGLYGLNTYRILEMETTHRLYSARGLEU
5   TYRASPGLULYSGLNGLNHISILEVALTYR
6   CYSSERASNASPLEULEUGLYASPLEUPHE
7   GLYVALPROSERPHESERVALLYSGLUHIS
8   ARGLYSILETYRTHRMETILETYRARGASN
9   LEUVALVAL

Samples:

sample_1: MCo-PMI 0.2 mM; Hdm2, [U-99% 13C; U-99% 15N], 0.2 mM; H2O 90%; D2O 10%

sample_2: MCo-PMI, [U-99% 15N], 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%

Sample_3: MCo-PMI 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.133 M; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYSample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

CHRMM v36, CHARMM-Karplus M. - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

PDB
BMRB 15945 18755 2410 6612
DBJ BAB11975 BAC78209 BAF83030 BAJ17752
EMBL CAA78055 CAD23251 CAD36959 CAH89564 CAP16708
GB AAA60568 AAF28866 AAF67833 AAG42840 AAG42841
PRF 1814460A
REF NP_001003103 NP_001009346 NP_001092577 NP_001098773 NP_001124685
SP P56950 P56951 Q00987 Q7YRZ8
TPG DAA29805