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- PDB-1r6n: HPV11 E2 TAD complex crystal structure -

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Basic information

Entry
Database: PDB / ID: 1r6n
TitleHPV11 E2 TAD complex crystal structure
ComponentsHPV11 REGULATORY PROTEIN E2
KeywordsTRANSCRIPTION / REPLICATION / Papillomavirus / E2 TAD / TAD / X-ray structure
Function / homology
Function and homology information


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
Chem-434 / 2-METHYL-PROPIONIC ACID / Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Y. / Coulombe, R.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the E2 Transactivation Domain of Human Papillomavirus Type 11 Bound to a Protein Interaction Inhibitor
Authors: Wang, Y. / Coulombe, R. / Cameron, D.R. / Thauvette, L. / Massariol, M.-J. / Amon, L.M. / Fink, D. / Titolo, S. / Welchner, E. / Yoakim, C. / Archambault, J. / White, P.W.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HPV11 REGULATORY PROTEIN E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8185
Polymers24,4351
Non-polymers1,3834
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.456, 60.456, 82.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Cell settingtetragonal
Space group name H-MP41

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Components

#1: Protein HPV11 REGULATORY PROTEIN E2 / HPV11 E2 TAD / E2 protein


Mass: 24434.838 Da / Num. of mol.: 1 / Fragment: TRANSACTIVATION DOMAIN (RESIDUES 2-201)
Source method: isolated from a genetically manipulated source
Details: inhibited form / Source: (gene. exp.) Human papillomavirus type 11 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 6 / Gene: E2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P04015
#2: Chemical ChemComp-434 / SPIRO[3-CARBOXY-4-{(4-[1,2,3]THIADIAZOL-4-YL-PHENYL)-AMINO-CARBONYL} -5-[3,4-DICHLORO-PHENYL]-TETRAHYDROFURAN-2,2'-5-METHYL-INDAN-1,3-DIONE] / BILH 434


Mass: 608.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H19Cl2N3O6S
#3: Chemical ChemComp-ALQ / 2-METHYL-PROPIONIC ACID


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.14 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Na Citrate, MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
160 mM1dropMe2SO
210 mg/mlHis-Lys-TAD1drop
30.1 Msodium citrate1reservoirpH5.5
435 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 11028 / Num. obs: 10792 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.44 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 27.47
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.01 / Num. unique all: 964 / % possible all: 86.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 11028 / Num. measured all: 70999
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HPV11 E2 TAb apo (1R6K)

1r6k


Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 879 -Random
Rwork0.2095 ---
all0.2095 11669 --
obs0.2095 11003 94.3 %-
Displacement parametersBiso mean: 60.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 92 27 1713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007251
X-RAY DIFFRACTIONc_angle_deg1.1901
X-RAY DIFFRACTIONc_dihedral_angle_d24.30859
X-RAY DIFFRACTIONc_improper_angle_d0.85799
X-RAY DIFFRACTIONc_mcbond_it1.566
X-RAY DIFFRACTIONc_mcangle_it2.741
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.30859
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85799

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