BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 19702

Title: Structure of the dimerization domain of the human polyoma, JC virus agnoprotein is an amphipathic alpha-helix.   PubMed: 24672035

Deposition date: 2013-12-23 Original release date: 2014-04-11

Authors: Coric, Pascale; Saribas, Sami; Abou-Gharbia, Magid; Childers, Wayne; White, Martyn; Bouaziz, Serge; Safak, Mahmut

Citation: Coric, Pascale; Sami Saribas, A.; Abou-Gharbia, Magid; Childers, Wayne; White, Martyn; Bouaziz, Serge; Safak, Mahmut. "Nuclear magnetic resonance structure revealed that human polyoma JC virus agnoprotein contains an alpha-helix encompassing the Leu/Ile/Phe-rich domain."  J. Virol. ., .-. (2014).

Assembly members:
AGNO, polymer, 36 residues, 4207.912 Da.

Natural source:   Common Name: JCV   Taxonomy ID: 10632   Superkingdom: Virus   Kingdom: not available   Genus/species: Polyomavirus JC polyomavirus

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
AGNO: TWSGTKKRAQRILIFLLEFL LDFCTGEDSVDGKKRQ

Data sets:
Data typeCount
1H chemical shifts256

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1AGNO protein1

Entities:

Entity 1, AGNO protein 36 residues - 4207.912 Da.

1   THRTRPSERGLYTHRLYSLYSARGALAGLN
2   ARGILELEUILEPHELEULEUGLUPHELEU
3   LEUASPPHECYSTHRGLYGLUASPSERVAL
4   ASPGLYLYSLYSARGGLN

Samples:

sample_1: AGNO 0.5 mM; H2O 70 v/v; TFE, [U-100% 2H], 30 v/v

sample_conditions_1: ionic strength: 0 M; pH: 3.0; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0 M; pH: 3.0; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0 M; pH: 3.0; pressure: 1 atm; temperature: 313 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1

Software:

TOPSPIN v1.3, Bruker Biospin - collection

CCPNMR_Analysis v2.2.2, CCPN - chemical shift assignment, data analysis, peak picking

ARIA v2.3.1, Linge, O, . - geometry optimization, refinement, structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAB11695 BAB11701 BAB11707 BAB11713 BAB11719
EMBL CDJ79842
GB AAA82098 AAB41702 AAB41708 AAB41714 AAB62681
REF NP_043508
SP P03086