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- PDB-1r8p: HPV-16 E2C solution structure -

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Basic information

Entry
Database: PDB / ID: 1r8p
TitleHPV-16 E2C solution structure
ComponentsRegulatory protein E2
KeywordsTRANSCRIPTION / dimeric beta-barrel / DNA binding protein / transcription factor
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain ...Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 16
MethodSOLUTION NMR / simulated annealing
AuthorsNadra, A.D. / Eliseo, T. / Cicero, D.O.
CitationJournal: J.Biomol.NMR / Year: 2004
Title: Solution structure of the HPV-16 E2 DNA binding domain, a transcriptional regulator with a dimeric beta-barrel fold
Authors: Nadra, A.D. / Eliseo, T. / Mok, Y.-K. / Almeida, C.L. / Bycroft, M. / Paci, M. / de Prat-Gay, G. / Cicero, D.O.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 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: Regulatory protein E2
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)18,7982
Polymers18,7982
Non-polymers00
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 #1closest to the average

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Components

#1: Protein Regulatory protein E2


Mass: 9398.914 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Gene: E2 / Plasmid: ptz18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P03120

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8mM 15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT95% H2O/5% D2O
20.9mM 13C,15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT95% H2O/5% D2O
30.2mM 15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT6% polyacrylamide gel
Sample conditionsIonic strength: 50mM Phosphate / pH: 6.5 / Pressure: ambient / Temperature: 303 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 AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE4002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
NMRPipe97.027.12.56Delaglio, F., et al.processing
NMRView5Johnson, B.A., et aldata analysis
X-PLOR3.85Brunger, A.T., et al.structure solution
X-PLOR3.85Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION PROTOCOL AND STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE IN THE JRNL RECORD.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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