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- PDB-1dto: CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PR... -

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Basic information

Entry
Database: PDB / ID: 1dto
TitleCRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PROTEIN FROM THE HUMAN PAPILLOMAVIRUS TYPE 16
ComponentsREGULATORY PROTEIN E2
KeywordsVIRAL PROTEIN / three-helix bundle / beta-sheet
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
E2 (early) protein, N terminal domain, subdomain 1 / Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein 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, N terminal domain, subdomain 1 / Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein 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 / Beta Complex / Helix Hairpins / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsAntson, A.A. / Burns, J.E. / Moroz, O.V. / Scott, D.J. / Sanders, C.M. / Bronstein, I.B. / Dodson, G.G. / Wilson, K.S. / Maitland, N.
Citation
Journal: Nature / Year: 2000
Title: Structure of the intact transactivation domain of the human papillomavirus E2 protein.
Authors: Antson, A.A. / Burns, J.E. / Moroz, O.V. / Scott, D.J. / Sanders, C.M. / Bronstein, I.B. / Dodson, G.G. / Wilson, K.S. / Maitland, N.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, Crystallisation and Preliminary X-ray Analysis of the E2 Transactivation Domain from Papillomavirus Type 16
Authors: Burns, J.E. / Moroz, O.V. / Antson, A.A. / Sanders, C.M. / Wilson, K.S. / Maitland, N.J.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)25,6991
Polymers25,6991
Non-polymers00
Water3,801211
1
A: REGULATORY PROTEIN E2

A: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)51,3982
Polymers51,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)54.680, 54.680, 155.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer constructed from chain A; the symmetry partner is generated by the crystallographic two-fold rotation X-Y,-Y,2/3-Z

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Components

#1: Protein REGULATORY PROTEIN E2


Mass: 25698.955 Da / Num. of mol.: 1 / Fragment: TRANSACTIVATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P03120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: monomethylether PEG 5000, NaCl, isopropanol, triethanolamine,Tris-HCl, DTT, EDTA, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.0-5.0 mg/mlprotein1drop
210 mMTris-HCl1drop
30.5 mMdithiothreitol1drop
40.2 mMEDTA1drop
5300 mM1dropNaCl
611 %mPEG50001reservoir
75-9 %isopropanol1reservoir
80.1 Mtriethanolamine1reservoir
9300 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 21751 / Num. obs: 21751 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.339 / Num. unique all: 837 / % possible all: 89.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 89.3 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 1.9→30 Å / SU B: 4.1 / SU ML: 0.121 / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.176 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1111 5 %Random
Rwork0.232 ---
all0.236 21748 --
obs0.236 21748 100 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 211 1861
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_plane_restr0.00960.02
X-RAY DIFFRACTIONp_chiral_restr0.1420.02
X-RAY DIFFRACTIONp_planar_tor5.25
X-RAY DIFFRACTIONp_staggered_tor16.820
X-RAY DIFFRACTIONp_transverse_tor26.130
X-RAY DIFFRACTIONp_mcbond_it1.131.5
X-RAY DIFFRACTIONp_mcangle_it1.712
X-RAY DIFFRACTIONp_scbond_it3.614
X-RAY DIFFRACTIONp_scangle_it4.896

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