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

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Basic information

Entry
Database: PDB / ID: 2jex
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: 2.35 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 24, 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)23,8211
Polymers23,8211
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.549, 60.549, 89.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein REGULATORY PROTEIN E2


Mass: 23820.590 Da / Num. of mol.: 1
Fragment: N-TERMINAL TRANS-ACTIVATION DOMAIN (TAD), RESIDUES 1-209
Mutation: YES
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.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 172 TO ALA

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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: 4.01 Å3/Da / Density % sol: 69.06 %
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, 2MM DTT 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: BM14 / Wavelength: 0.919
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 14352 / % possible obs: 93.3 % / Observed criterion σ(I): 3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JEU

2jeu


Resolution: 2.35→22.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.331 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 716 5 %RANDOM
Rwork0.21 ---
obs0.211 13541 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.35→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 0 115 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9292172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47223.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53115271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9741513
X-RAY DIFFRACTIONr_chiral_restr0.080.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2702
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21081
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.69321004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24831555
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.796713
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.20910617
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: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 54 -
Rwork0.275 981 -
obs--100 %
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)
111.57861.40952.67593.67941.19816.37860.03570.15630.792-0.0054-0.03110.3935-0.56150.0122-0.0046-0.302-0.06060.094-0.10070.0818-0.2527-11.4634-2.94724.4717
23.4763-0.6418-3.04671.44690.86788.67890.0609-0.8631-0.3080.1575-0.1671-0.04410.28530.5510.1062-0.31670.0186-0.02580.09760.0479-0.073615.8066-8.7422-3.9543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 95
2X-RAY DIFFRACTION2A96 - 199

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