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- PDB-2jeu: Transcription activator structure reveals redox control of a repl... -

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Basic information

Entry
Database: PDB / ID: 2jeu
TitleTranscription activator structure reveals redox control of a replication initiation reaction
ComponentsREGULATORY PROTEIN E2
KeywordsTRANSCRIPTION / NUCLEAR PROTEIN / DNA REPLICATION / PHOSPHORYLATION / TRANSCRIPTION REGULATION / VIRAL TRANSCRIPTION FACTOR / BOVINE PAPILLOMAVIRUS / REPLICATION INITIATION / EARLY PROTEIN / REDOX CONTROL / E1 / E2 / OXIDATION / ACTIVATOR / REPRESSOR / DNA-BINDING
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
Regulatory protein E2
Similarity search - Component
Biological speciesBOVINE PAPILLOMAVIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSanders, C.M. / Sizov, D. / Seavers, P.R. / Ortiz-Lombardia, M. / Antson, A.A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Transcription Activator Structure Reveals Redox Control of a Replication Initiation Reaction.
Authors: Sanders, C.M. / Sizov, D. / Seavers, P.R. / Ortiz-Lombardia, M. / Antson, A.A.
History
DepositionJan 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)23,9071
Polymers23,9071
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.539, 61.539, 236.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein REGULATORY PROTEIN E2


Mass: 23906.705 Da / Num. of mol.: 1
Fragment: N-TERMINAL TRANS-ACTIVATION DOMAIN (TAD), RESIDUES 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE PAPILLOMAVIRUS TYPE 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03122
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.71 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN WAS CRYSTALLISED FROM 0.1 M TRIS-HCL PH 8.5, 0.3 M NACL AND 18-22% TERTIARY BUTANOL, USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 7171 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DTO

1dto


Resolution: 2.8→24.33 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 38.118 / SU ML: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.826 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 500 7 %RANDOM
Rwork0.233 ---
obs0.236 6594 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å2-1.5 Å20 Å2
2---3.01 Å20 Å2
3---4.51 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 0 17 1595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.9292179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29623.2181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1641514
X-RAY DIFFRACTIONr_chiral_restr0.070.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2650
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21081
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4411.5995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8931556
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.454717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4388623
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 33
Rwork0.27 412
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.0385-0.84975.31753.3662-0.07187.2397-0.38661.01660.6518-0.4413-0.041-0.1944-0.51940.17320.4276-0.1607-0.0590.117-0.0556-0.0854-0.29675.596538.955126.8391
25.03430.5482-2.52434.1255-1.62646.0911-0.24380.4132-0.0132-0.0101-0.21010.4078-0.1821-0.17090.4539-0.3159-0.0033-0.02830.1051-0.32590.0711-22.042532.7291134.4818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 95
2X-RAY DIFFRACTION2A96 - 199

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