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- PDB-2fk4: Solution structure of the C-terminal zinc binding domain of the H... -

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Basic information

Entry
Database: PDB / ID: 2fk4
TitleSolution structure of the C-terminal zinc binding domain of the HPV16 E6 oncoprotein
ComponentsProtein E6
KeywordsMetal binding protein / Oncoprotein / ZINC BINDING DOMAIN
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
E6 early regulatory protein / CRO Repressor / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman papillomavirus type 16
MethodSOLUTION NMR / simulated annealing, protocol refine.inp
AuthorsNomine, Y. / Charbonnier, S.
Citation
Journal: Mol.Cell / Year: 2006
Title: Structural and functional analysis of E6 oncoprotein: insights in the molecular pathways of human papillomavirus-mediated pathogenesis
Authors: Nomine, Y. / Masson, M. / Charbonnier, S. / Zanier, K. / Ristriani, T. / Deryckere, F. / Sibler, A.P. / Desplancq, D. / Atkinson, R.A. / Weiss, E. / Orfanoudakis, G. / Kieffer, B. / Trave, G.
#1: Journal: J.Biomol.Nmr / Year: 2005
Title: 1H and 15N resonance assignment, secondary structure and dynamic behaviour of the C-terminal domain of human papillomavirus oncoprotein E6.
Authors: Charbonnier, S. / Miguet, L. / Potier, N. / Van Dorsselaer, A. / Atkinson, R.A. / Kieffer, B.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9712
Polymers8,9051
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Protein E6


Mass: 8905.230 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Mutation: C4S, C20S, C34S, C63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE2 / References: UniProt: P03126
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2222D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D 15N heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM E6C U-15N; 20 mM TRIS-HCl, 50 mM NaCl, 1mM DTT90% H2O/10% D2O
21.0 mM E6C, 20 mM TRIS-HCl, 50 mM NaCl, 1mM DTT90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 6.8 ambient 288 K
250 mM 6.8 ambient 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIHBrungerstructure solution
XEASY1Bartelsdata analysis
XwinNMR2.6Brukerprocessing
X-PLORNIHBrungerrefinement
RefinementMethod: simulated annealing, protocol refine.inp / Software ordinal: 1
Details: NOE distance restraints were split in two sets. One set involved residues that were identified as beeing affected by conformational exchange by relaxation dispersion experiments. These ...Details: NOE distance restraints were split in two sets. One set involved residues that were identified as beeing affected by conformational exchange by relaxation dispersion experiments. These distances were assigned an additional 1A to the upper distance limit. Reported close contacts are due to conformational heterogeneities in the set of NOES. The dynamical properties of this protein have been described in depth in the J. Biomol. NMR reference cited above.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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