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- PDB-2aye: Crystal structure of the unliganded E2 DNA Binding Domain from HPV6a -

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Basic information

Entry
Database: PDB / ID: 2aye
TitleCrystal structure of the unliganded E2 DNA Binding Domain from HPV6a
ComponentsRegulatory protein E2
KeywordsTRANSCRIPTION / beta barrel
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
Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein E2
B: Regulatory protein E2
C: Regulatory protein E2
D: Regulatory protein E2
E: Regulatory protein E2
F: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,05823
Polymers61,4456
Non-polymers1,61317
Water2,666148
1
A: Regulatory protein E2
B: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1429
Polymers20,4822
Non-polymers6617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-79 kcal/mol
Surface area9040 Å2
MethodPISA
2
C: Regulatory protein E2
D: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0548
Polymers20,4822
Non-polymers5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-81 kcal/mol
Surface area9210 Å2
MethodPISA
3
E: Regulatory protein E2
F: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8626
Polymers20,4822
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-64 kcal/mol
Surface area9090 Å2
MethodPISA
4
A: Regulatory protein E2
B: Regulatory protein E2
hetero molecules

E: Regulatory protein E2
F: Regulatory protein E2
hetero molecules

C: Regulatory protein E2
D: Regulatory protein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,05823
Polymers61,4456
Non-polymers1,61317
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area14240 Å2
ΔGint-266 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.766, 106.886, 74.945
Angle α, β, γ (deg.)90.00, 121.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41A
51C
61E
71A
81C
91E
12B
22D
32F
42B
52D
62F

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALATRPTRPAA283 - 3193 - 40
211ALAALATRPTRPCC283 - 3193 - 40
311ALAALATRPTRPEE283 - 3193 - 40
421ALAALAILEILEAA329 - 35050 - 71
521ALAALAILEILECC329 - 35050 - 71
621ALAALAILEILEEE329 - 35050 - 71
731ILEILELEULEUAA354 - 36675 - 87
831ILEILELEULEUCC354 - 36675 - 87
931ILEILELEULEUEE354 - 36675 - 87
112ALAALAALAALABB283 - 3203 - 41
212ALAALAALAALADD283 - 3203 - 41
312ALAALAALAALAFF283 - 3203 - 41
422ALAALALEULEUBB329 - 36650 - 87
522ALAALALEULEUDD329 - 36650 - 87
622ALAALALEULEUFF329 - 36650 - 87

NCS ensembles :
ID
1
2
Detailsbiological assembly is a dimer - chains A and B, chains C and D, chains E and F

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Components

#1: Protein
Regulatory protein E2


Mass: 10240.854 Da / Num. of mol.: 6 / 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: pKK-223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q84294
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, Tris, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.284 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 25, 2005 / Details: mirrors
RadiationMonochromator: Rh coated collimating mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 2.3→65.65 Å / Num. all: 28323 / Num. obs: 26868 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.051 / Χ2: 2.723 / Net I/σ(I): 37.3
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 96.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 5.5 / Num. measured obs: 2181 / Χ2: 0.859 / % possible all: 82.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Code 1R8H

1r8h


Resolution: 2.3→65.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.745 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1445 5.1 %RANDOM
Rwork0.185 ---
all0.189 26877 --
obs0.23 26868 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.285 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-1.44 Å2
2---2.29 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 90 148 4558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214545
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9326158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5015518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7422.311212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.615773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1151530
X-RAY DIFFRACTIONr_chiral_restr0.1540.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023394
X-RAY DIFFRACTIONr_nbd_refined0.2250.21899
X-RAY DIFFRACTIONr_nbtor_refined0.30.22895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.430.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.212
X-RAY DIFFRACTIONr_mcbond_it1.0851.52715
X-RAY DIFFRACTIONr_mcangle_it1.73724286
X-RAY DIFFRACTIONr_scbond_it2.45332086
X-RAY DIFFRACTIONr_scangle_it3.4094.51870
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberRmsTypeWeight
11A6210.49LOOSE POSITIONAL5
12C6210.47LOOSE POSITIONAL5
13E6210.7LOOSE POSITIONAL5
11A6215.04LOOSE THERMAL10
12C6213.32LOOSE THERMAL10
13E6217.23LOOSE THERMAL10
21B6390.6LOOSE POSITIONAL5
22D6390.42LOOSE POSITIONAL5
23F6390.47LOOSE POSITIONAL5
21B6393.86LOOSE THERMAL10
22D6395.17LOOSE THERMAL10
23F6393.14LOOSE THERMAL10
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 86 -
Rwork0.209 1638 -
all-1724 -
obs--80.45 %
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)
12.7948-0.02370.48771.464-0.19921.58310.08860.0036-0.03590.004-0.02230.08290.0305-0.0259-0.0663-0.0290.0353-0.04-0.0643-0.0225-0.0853-23.657227.471215.1827
22.84210.55241.62212.35270.52272.96330.12140.1361-0.1708-0.1901-0.0333-0.1380.02240.2474-0.0881-0.0740.0391-0.0079-0.0693-0.0356-0.0843-4.573329.829422.0402
32.3895-0.54780.95173.799-0.40062.61080.04990.073-0.043-0.3428-0.00050.13180.0512-0.1833-0.0495-0.08550.0562-0.0602-0.05780.0118-0.0842-43.569742.528117.5627
41.81960.1960.48738.5635-0.27732.21410.1186-0.07070.1762-0.31-0.0967-0.3958-0.40130.0898-0.0219-0.06330.06030.0292-0.13260.0409-0.0429-35.66660.775816.4221
53.666-1.351-0.76588.57682.2684.0351-0.1995-0.02760.19750.7987-0.07670.36490.3012-0.41410.27620.0042-0.0320.0863-0.0582-0.0562-0.148214.340754.327516.8465
62.8342-0.615-0.69143.4631.6582.224-0.1392-0.17380.10010.50180.1639-0.14070.45420.0118-0.02470.0087-0.009-0.0537-0.0432-0.0107-0.126226.587439.931510.1141
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 283 - 366 / Label seq-ID: 3 - 87

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

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