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- PDB-1jj4: Human papillomavirus type 18 E2 DNA-binding domain bound to its D... -

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Basic information

Entry
Database: PDB / ID: 1jj4
TitleHuman papillomavirus type 18 E2 DNA-binding domain bound to its DNA target
Components
  • E2 binding site DNA
  • Regulatory protein E2
KeywordsTRANSCRIPTION/DNA / HPV-18 / E2 / DNA-binding domain / E2-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / host cell mitochondrial membrane / 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
DNA / DNA (> 10) / Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 18
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, S.-S. / Tam, J.K. / Wang, A.F. / Hegde, R.S.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structural basis of DNA target discrimination by papillomavirus E2 proteins.
Authors: Kim, S.S. / Tam, J.K. / Wang, A.F. / Hegde, R.S.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: E2 binding site DNA
D: E2 binding site DNA
A: Regulatory protein E2
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)28,9744
Polymers28,9744
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.880, 82.190, 96.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthe biological assembly is a homodimer

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Components

#1: DNA chain E2 binding site DNA


Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Regulatory protein E2


Mass: 9588.977 Da / Num. of mol.: 2 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: E2 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06790
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: MPD, sodium acetate, calcium chloride, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium acetate11
3CaCl211
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMTris-HCl1drop
2100 mM1dropNaCl
310 mMdithiothreitol1drop
410 mg/mlprotein1drop
547 %MPD1reservoir
6100 mMsodium acetate1reservoir
720 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 12652 / Num. obs: 11109 / % possible obs: 87.8 % / Redundancy: 4.27 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.33 / Num. unique all: 1107 / % possible all: 89.2
Reflection
*PLUS
Lowest resolution: 99 Å
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
RAXCTRLV. 6.5data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.65 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 374703.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.287 957 10.3 %RANDOM
Rwork0.21 ---
obs0.21 9277 83.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3429 Å2 / ksol: 0.310716 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.85 Å20 Å20 Å2
2--3.14 Å20 Å2
3----10.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 650 0 190 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_mcangle_it1.22
X-RAY DIFFRACTIONc_scbond_it0.62
X-RAY DIFFRACTIONc_scangle_it0.942.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 171 11.5 %
Rwork0.303 1313 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10.3 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.383 / % reflection Rfree: 11.5 % / Rfactor Rwork: 0.303

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