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- PDB-2m3l: Solution structure of the C-terminal zinc-binding domain of HPV51... -

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Basic information

Entry
Database: PDB / ID: 2m3l
TitleSolution structure of the C-terminal zinc-binding domain of HPV51 oncoprotein E6
ComponentsProtein E6
KeywordsONCOPROTEIN / Papillomavirus E6 Proteins / HPV / Oncoprotein E6 / Zinc Fingers / E6 / Viral / Oncogene Proteins
Function / homology
Function and homology information


regulation of proteolysis / : / 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 / DNA-templated transcription / host cell nucleus / regulation of DNA-templated transcription ...regulation of proteolysis / : / 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 / DNA-templated transcription / host cell nucleus / regulation of DNA-templated transcription / DNA 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 51
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsMischo, A. / Ohlenschlager, O. / Gorlach, M.
CitationJournal: Plos One / Year: 2013
Title: Structural insights into a wildtype domain of the oncoprotein E6 and its interaction with a PDZ domain.
Authors: Mischo, A. / Ohlenschlager, O. / Hortschansky, P. / Ramachandran, R. / Gorlach, M.
History
DepositionJan 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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 / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_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

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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)9,0172
Polymers8,9511
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein E6


Mass: 8951.210 Da / Num. of mol.: 1 / Fragment: E6, UNP residues 80-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 51 / Strain: TYPE 51 / Gene: E6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P26554
#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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNHA
1613D 1H-15N NOESY
1723D 1H-13C HSQC NOESY aliphatic
1823D 1H-13C NOESY aromatic
1923D (H)CCH-COSY
11013D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.13 mM [U-100% 13C; U-100% 15N] E6, 90 mM sodium chloride, 45 mM L-arginine, 45 mM L-glutamate, 9 mM DTT, 0.05 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-100% 13C; U-100% 15N] E6, 90 mM sodium chloride, 45 mM L-arginine, 45 mM L-glutamate, 9 mM DTT, 0.05 w/v sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.13 mME6-1[U-100% 13C; U-100% 15N]1
90 mMsodium chloride-21
45 mML-arginine-31
45 mML-glutamate-41
9 mMDTT-51
0.05 w/vsodium azide-61
0.9 mME6-7[U-100% 13C; U-100% 15N]2
90 mMsodium chloride-82
45 mML-arginine-92
45 mML-glutamate-102
9 mMDTT-112
0.05 w/vsodium azide-122
Sample conditionsIonic strength: 180 / pH: 7.4 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAVANCE III7501
Bruker AvanceIIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CARAKeller and Wuthrichdata analysis
TopSpinBruker Biospincollection & processing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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