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- PDB-2b9d: Crystal Structure of HPV E7 CR3 domain -

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Basic information

Entry
Database: PDB / ID: 2b9d
TitleCrystal Structure of HPV E7 CR3 domain
ComponentsE7 protein
Keywordstranscription / viral protein / Zinc Finger / Homodimer
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA-binding transcription factor activity / protein domain specific binding / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding
Similarity search - Function
Double Stranded RNA Binding Domain - #330 / Papillomavirus E7 / E7 protein, Early protein / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman papillomavirus type 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLiu, X. / Clements, A. / Zhao, K. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the human Papillomavirus E7 oncoprotein and its mechanism for inactivation of the retinoblastoma tumor suppressor.
Authors: Liu, X. / Clements, A. / Zhao, K. / Marmorstein, R.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: 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: Refinement description / Category: 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E7 protein
B: E7 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9854
Polymers11,8542
Non-polymers1312
Water1,58588
1
A: E7 protein
hetero molecules

A: E7 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9854
Polymers11,8542
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
2
B: E7 protein
hetero molecules

B: E7 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9854
Polymers11,8542
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)33.908, 44.935, 58.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1036-

HOH

21A-1050-

HOH

DetailsEach Asymmetric unit contains two subunits, and the biological homodimer is formed by two subunits from different asymmetric unit

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Components

#1: Protein E7 protein


Mass: 5927.104 Da / Num. of mol.: 2 / Fragment: CR3 Domain (residues 44-93)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 1a / Genus: Mupapillomavirus / Species: Human papillomavirus - 1 / Plasmid: pRSET-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06465
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.28
SYNCHROTRONAPS 19-ID21.2832, 1.2836, 1.2800
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJun 11, 2003
CUSTOM-MADE2CCDJun 11, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.281
21.28321
31.28361
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
173920.0471.0642.325097.5
273690.0491.0212.325098.3
374720.0530.9752.315096.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
55094.910.0461.038
3.97599.710.041.115
3.473.9799.910.041.011
3.153.4799.610.0441.079
2.923.1599.710.0481.138
2.752.9299.310.0561.116
2.612.7599.210.0651.03
2.52.6199.710.0721.031
2.42.59810.0811.004
2.322.485.610.0881.078
55095.420.0461.1
3.97599.620.0390.966
3.473.9799.920.0391.079
3.153.4799.620.0441.116
2.923.1599.620.0491.038
2.752.9299.320.0610.978
2.612.7599.220.0790.976
2.52.6199.720.0870.968
2.42.597.720.1010.957
2.322.493.420.1141.035
4.985096.230.0471.135
3.954.9899.730.040.959
3.453.9599.730.0421.055
3.133.4599.730.0481.068
2.913.1399.630.0570.935
2.742.9199.430.0770.886
2.62.749930.1040.954
2.492.698.430.1220.883
2.392.4997.130.140.916
2.312.3974.630.1430.923
ReflectionResolution: 1.6→50 Å / Num. obs: 12140 / % possible obs: 98.2 % / Rmerge(I) obs: 0.08
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID
1.6-1.660.3351,2
1.66-1.720.2971,2
1.72-1.80.2541,2
1.8-1.90.1971,2
1.9-2.020.1351,2
2.02-2.170.1011,2
2.17-2.390.0811,2
2.39-2.740.0751,2
2.74-3.450.0621,2
3.45-500.0541,2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.280.8-6
13 wavelength21.28362.4-9.8
13 wavelength31.28324.4-8.2
Phasing dmFOM : 0.73 / FOM acentric: 0.76 / FOM centric: 0.6 / Reflection: 3921 / Reflection acentric: 3137 / Reflection centric: 784
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-29.4620.830.920.7119110982
4.1-6.60.870.910.75554397157
3.3-4.10.830.860.72647497150
2.9-3.30.780.830.58674547127
2.5-2.90.670.70.4711771001176
2.3-2.50.540.570.3567858692

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.29 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25232 1188 9.8 %RANDOM
Rwork0.20835 ---
obs0.21246 10931 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.918 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---0.06 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 2 88 890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022808
X-RAY DIFFRACTIONr_bond_other_d0.0010.02788
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.9951096
X-RAY DIFFRACTIONr_angle_other_deg0.57831828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7055102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02864
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02142
X-RAY DIFFRACTIONr_nbd_refined0.2350.3178
X-RAY DIFFRACTIONr_nbd_other0.2620.3937
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.5562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.588
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.398
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.0951.5522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.9972842
X-RAY DIFFRACTIONr_scbond_it18.2413286
X-RAY DIFFRACTIONr_scangle_it26.4784.5254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 97
Rwork0.242 753
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)
12.04880.1539-0.10591.47570.44711.96140.1615-0.00960.0297-0.07550.0202-0.05460.01630.0174-0.18170.0833-0.00510.02610.01630.00020.040719.43126.52938.699
22.7372-1.0851-0.24272.9739-0.38351.0801-0.2179-0.2986-0.30840.24270.25480.22890.0695-0.0908-0.03690.00670.00650.01580.0860.02250.037914.26741.40850.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA42 - 931 - 52
2X-RAY DIFFRACTION2BB42 - 931 - 52

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