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- PDB-2nnu: Crystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4 -

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Basic information

Entry
Database: PDB / ID: 2nnu
TitleCrystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4
Components
  • Bromodomain-containing protein 4BRD4
  • Regulatory protein E2
KeywordsTRANSCRIPTION / Protein-peptide complex / Helical peptide / three helix bundle / amphipathic helix
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / regulation of DNA replication / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity ...host cytoskeleton / viral DNA genome replication / regulation of DNA replication / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / DNA replication / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / DNA damage response / chromatin binding / host cell nucleus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
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 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Beta Complex / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Helix Hairpins / Bromodomain-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 16
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsAbbate, E.A. / Voitenleitner, C. / Botchan, M.R.
CitationJournal: Mol.Cell / Year: 2006
Title: Structure of the Papillomavirus DNA-Tethering Complex E2:Brd4 and a Peptide that Ablates HPV Chromosomal Association.
Authors: Abbate, E.A. / Voitenleitner, C. / Botchan, M.R.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Regulatory protein E2
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)26,3082
Polymers26,3082
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area12910 Å2
MethodPISA
2
A: Regulatory protein E2
B: Bromodomain-containing protein 4

A: Regulatory protein E2
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)52,6154
Polymers52,6154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5920 Å2
ΔGint-26 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.892, 94.589, 119.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Regulatory protein E2


Mass: 23815.844 Da / Num. of mol.: 1 / Fragment: Activation Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Gene: E2 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P03120
#2: Protein/peptide Bromodomain-containing protein 4 / BRD4 / HUNK1 protein


Mass: 2491.726 Da / Num. of mol.: 1 / Fragment: C-terminal residues (1343-1362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: O60885
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM citrate, 1.8-2.0M Na-acetate, 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 40019 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.6
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 3691 / Rsym value: 0.207 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DTO

1dto


Resolution: 1.59→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.376 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23331 2025 5.1 %RANDOM
Rwork0.19963 ---
obs0.20133 37969 98.37 %-
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: 24.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 0 210 2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9252524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3445219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3462596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.134155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021409
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2817
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21263
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4451.51120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13121783
X-RAY DIFFRACTIONr_scbond_it3.2073842
X-RAY DIFFRACTIONr_scangle_it4.7694.5741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 149 -
Rwork0.256 2530 -
obs--90.84 %

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