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- PDB-2ayb: Crystal structure of HPV6a E2 DNA Binding Domain bound to a 16 ba... -

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Basic information

Entry
Database: PDB / ID: 2ayb
TitleCrystal structure of HPV6a E2 DNA Binding Domain bound to a 16 base pair DNA target
Components
  • 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'
  • Regulatory protein E2
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / double helix / beta barrel / TRANSCRIPTION-DNA COMPLEX
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
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 6a
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHooley, E. / Brady, R.L. / Gaston, K.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein.
Authors: Hooley, E. / Fairweather, V. / Clarke, A.R. / Gaston, K. / Brady, R.L.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 23, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'
D: 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'
A: Regulatory protein E2
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)30,2784
Polymers30,2784
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.247, 75.247, 97.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 283 - 364 / Label seq-ID: 3 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AC
2BD
DetailsThe biological assembly is a protein dimer bound to double stranded DNA

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Components

#1: DNA chain 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'


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


Mass: 10240.854 Da / Num. of mol.: 2 / Fragment: C Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 6a / Genus: Alphapapillomavirus / Species: Human papillomavirus - 6 / Gene: E2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1-blue / References: UniProt: Q84294
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1tri-Sodium citrate dihydrate11
2H2O11
3tri-Sodium citrate dihydrate12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.548 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 20, 2005 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 3.2→65.23 Å / Num. all: 5168 / Num. obs: 4928 / % possible obs: 99.37 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.5 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 19.8
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.2 / Num. unique all: 362 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Protein of PDB entry 1R8H DNA of PDB entry 1JJ4

1r8h

1jj4


Resolution: 3.2→65.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.843 / SU B: 33.517 / SU ML: 0.402 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 240 4.6 %RANDOM
Rwork0.189 ---
all0.194 4928 --
obs0.259 4928 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å21.1 Å20 Å2
2--2.2 Å20 Å2
3----3.31 Å2
Refinement stepCycle: LAST / Resolution: 3.2→65.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 650 0 12 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212218
X-RAY DIFFRACTIONr_angle_refined_deg2.1482.3033138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0675172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31822.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.96615258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6881510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021456
X-RAY DIFFRACTIONr_nbd_refined0.250.21024
X-RAY DIFFRACTIONr_nbtor_refined0.320.21414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.24
X-RAY DIFFRACTIONr_mcbond_it0.5521.5891
X-RAY DIFFRACTIONr_mcangle_it1.0221430
X-RAY DIFFRACTIONr_scbond_it1.02131696
X-RAY DIFFRACTIONr_scangle_it1.7424.51708
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 693 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.02TIGHT POSITIONAL0.05
0.03TIGHT THERMAL0.5
LS refinement shellResolution: 3.204→3.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 16 -
Rwork0.266 362 -
obs--98.95 %
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)
12.0086-0.31970.19512.4985-0.1692.7172-0.15160.2636-0.2337-0.14940.15380.04330.33870.0745-0.00220.0067-0.06720.08080.0851-0.0142-0.0595-13.60718.0505-14.8703
22.4077-0.5251-0.27871.79720.23563.20640.086-0.2957-0.0930.0453-0.1333-0.22170.19750.25420.04730.0014-0.07330.02640.07050.0793-0.0412-8.845420.8863.3446
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 281 - 366 / Label seq-ID: 1 - 87

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11BD
22AC

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