BMRB Entry 17968

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17968
MolProbity Validation Chart

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Title:
Haddock model structure of the N-terminal domain dimer of HPV16 E6
Deposition date:
2011-09-30
Original release date:
2012-04-04
Authors:
Zanier, Katia; ould M'hamed ould Sidi, Abdellahi; Boulade-Ladame, Charlotte; Rybin, Vladimir; Chappelle, Anne; Atkinson, Andrew; Kieffer, Bruno; Trave, Gilles
Citation:

Citation: Zanier, Katia; Boulade-Ladame, Abdellahi; Rybin, Charlotte; Chappelle, Vladimir; Atkinson, Anne; Kieffer, Andrew; Trave, Bruno. "Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53."  Structure 20, 604-617 (2012).
PubMed: 22483108

Assembly members:

Assembly members:
HPV16_E6, polymer, 82 residues, 8505.967 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Human papillomavirus type 16   Taxonomy ID: 333760   Superkingdom: Viruses   Kingdom: not available   Genus/species: Alphapapillomavirus Human papillomavirus 16

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: petM41

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HPV16_E6: GAMFQDPQERPRKLPQLCTE LQTTIHDIILECVYCKQQLL RREVYDFAFRDLCIVYRDGN PYAVCDKCLKFYSKISEYRH YS

Data sets:
Data typeCount
13C chemical shifts259
15N chemical shifts83
1H chemical shifts549

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1HPV_16_E6_11
2HPV_16_E6_21
3ZINC ION_12
4ZINC ION_22

Entities:

Entity 1, HPV_16_E6_1 82 residues - 8505.967 Da.

The natural E6 sequence starts at M1. Residues G-1 and A0 are introduced by colning. Residues G-1 to A0 and S71 to S80 are not displayed in the coordinate file because unstructured.

1   GLYALAMETPHEGLNASPPROGLNGLUARG
2   PROARGLYSLEUPROGLNLEUCYSTHRGLU
3   LEUGLNTHRTHRILEHISASPILEILELEU
4   GLUCYSVALTYRCYSLYSGLNGLNLEULEU
5   ARGARGGLUVALTYRASPPHEALAPHEARG
6   ASPLEUCYSILEVALTYRARGASPGLYASN
7   PROTYRALAVALCYSASPLYSCYSLEULYS
8   PHETYRSERLYSILESERGLUTYRARGHIS
9   TYRSER

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

E6_unl: HPV16_E6 0.3 mM; H2O 90%; D2O 10%; NaCl 50 mM

E6_N: E6, [U-100% 15N], 0.3 mM; H2O 90%; D2O 10%; NaCl 50 mM

E6_CN: E6, [U-100% 13C; U-100% 15N], 0.3 mM; H2O 90%; D2O 10%; NaCl 50 mM

E6: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 296 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCE6_NisotropicE6
2D 1H-13C HSQC aliphaticE6_CNisotropicE6
2D 1H-13C HSQC aromaticE6_CNisotropicE6
3D HNCAE6_CNisotropicE6
3D HNCACBE6_CNisotropicE6
3D HN(CO)CAE6_CNisotropicE6
3D HCCH-TOCSYE6_CNisotropicE6
3D HCCH-COSYE6_CNisotropicE6
3D 1H-15N NOESYE6_NisotropicE6
3D 1H-13C NOESY aliphaticE6_CNisotropicE6
2D 1H-1H NOESYE6_unlisotropicE6
2D 1H-1H NOESYE6_unlisotropicE6

Software:

TOPSPIN v2.1, Bruker Biospin - collection

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

CARA v1.8.3, Keller and Wuthrich - data analysis

HADDOCK_webserver, Utrecht Biomolecular Interaction web portal - structure calculation

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker Avance 700 MHz

Related Database Links:

BMRB 17967
PDB
DBJ BAN15903 BAN15904 BAN15905 BAN15906 BAN15907
EMBL CAB45104 CAB45106 CAB45108 CAB45110 CAB45112
GB AAA46939 AAA91654 AAA91655 AAA91656 AAA91657
REF NP_041325
SP P03126
AlphaFold P03126

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