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- PDB-1tue: The X-ray Structure of the Papillomavirus Helicase in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 1tue
TitleThe X-ray Structure of the Papillomavirus Helicase in Complex with its Molecular Matchmaker E2
Components
  • Regulatory protein E2
  • Replication protein E1DNA replication
KeywordsREPLICATION / Human papillomavirus / helicase / E1E2 complex / AAA+ protein
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / host cell mitochondrial membrane / regulation of DNA replication / DNA helicase activity / viral genome replication / DNA helicase / host cell cytoplasm / DNA replication / DNA-binding transcription factor activity ...host cytoskeleton / viral DNA genome replication / host cell mitochondrial membrane / regulation of DNA replication / DNA helicase activity / viral genome replication / DNA helicase / host cell cytoplasm / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
E2 (early) protein, N terminal domain, subdomain 1 / Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein domain / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain ...E2 (early) protein, N terminal domain, subdomain 1 / Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein domain / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding 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 / Zinc finger, large T-antigen D1 domain superfamily / E2/EBNA1, C-terminal / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Beta Complex / Helix Hairpins / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Replication protein E1 / Regulatory protein E2 / Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsAbbate, E.A. / Berger, J.M. / Botchan, M.R.
CitationJournal: Genes Dev. / Year: 2004
Title: The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2
Authors: Abbate, E.A. / Berger, J.M. / Botchan, M.R.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Replication protein E1
B: Regulatory protein E2
D: Replication protein E1
E: Regulatory protein E2
F: Replication protein E1
G: Regulatory protein E2
H: Replication protein E1
J: Regulatory protein E2
K: Replication protein E1
L: Regulatory protein E2
M: Replication protein E1
Q: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)298,21712
Polymers298,21712
Non-polymers00
Water17,457969
1
A: Replication protein E1
B: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Replication protein E1
E: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Replication protein E1
G: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Replication protein E1
J: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: Replication protein E1
L: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
M: Replication protein E1
Q: Regulatory protein E2


Theoretical massNumber of molelcules
Total (without water)49,7032
Polymers49,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.297, 88.745, 375.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are six copies of the biological assembly in the assymetric unit.

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Components

#1: Protein
Replication protein E1 / DNA replication


Mass: 24617.115 Da / Num. of mol.: 6 / Mutation: C14A,V15L,R90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: E1 / Plasmid: pMALc2 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P06789
#2: Protein
Regulatory protein E2


Mass: 25085.650 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: E2 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q80B71, UniProt: P06790*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6
Details: 7-10% PEG 3,350, 50mM MES, 20-40mM MgCl, pH 6.0, Microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.483,1.501
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4831
21.5011
ReflectionResolution: 2.1→50 Å / Num. obs: 161300 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rsym value: 0.049
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rsym value: 0.379 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 8003 5 %RANDOM
Rwork0.2188 ---
all0.22098 ---
obs0.22098 151539 99.04 %-
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: 40.459 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19217 0 0 969 20186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02219784
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.90426849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12452318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34724.3761010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.293153251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4111579
X-RAY DIFFRACTIONr_chiral_restr0.0730.22801
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215273
X-RAY DIFFRACTIONr_nbd_refined0.1960.28881
X-RAY DIFFRACTIONr_nbtor_refined0.3050.213475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.2156
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.256
X-RAY DIFFRACTIONr_mcbond_it0.6091.511632
X-RAY DIFFRACTIONr_mcangle_it1.145218841
X-RAY DIFFRACTIONr_scbond_it1.33238152
X-RAY DIFFRACTIONr_scangle_it2.1064.58008
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 576 -
Rwork0.266 10003 -
obs--90.23 %

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