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- PDB-2gxa: Crystal structure of papillomavirus E1 hexameric helicase with ss... -

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Basic information

Entry
Database: PDB / ID: 2gxa
TitleCrystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • Replication protein E1
Keywordsreplication/DNA / DNA helicase / AAA+ / ATPase / replication / virus / initiator protein / replication-DNA COMPLEX
Function / homology
Function and homology information


DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Zinc finger, large T-antigen D1 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 / Zinc finger, large T-antigen D1 domain superfamily ...Zinc finger, large T-antigen D1 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 / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Replication protein E1
Similarity search - Component
Biological speciesBovine papillomavirus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsEnemark, E.J. / Joshua-Tor, L.
CitationJournal: Nature / Year: 2006
Title: Mechanism of DNA translocation in a replicative hexameric helicase.
Authors: Enemark, E.J. / Joshua-Tor, L.
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: 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 ...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_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.ptnr2_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
N: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
A: Replication protein E1
B: Replication protein E1
C: Replication protein E1
D: Replication protein E1
E: Replication protein E1
F: Replication protein E1
G: Replication protein E1
H: Replication protein E1
I: Replication protein E1
J: Replication protein E1
K: Replication protein E1
L: Replication protein E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,34938
Polymers381,30014
Non-polymers5,04924
Water27015
1
M: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
A: Replication protein E1
B: Replication protein E1
C: Replication protein E1
D: Replication protein E1
E: Replication protein E1
F: Replication protein E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,40620
Polymers190,6507
Non-polymers2,75613
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
G: Replication protein E1
H: Replication protein E1
I: Replication protein E1
J: Replication protein E1
K: Replication protein E1
L: Replication protein E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,94318
Polymers190,6507
Non-polymers2,29311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.510, 100.881, 125.023
Angle α, β, γ (deg.)92.60, 111.46, 106.01
Int Tables number1
Space group name H-MP1
DetailsThe structure consists of 2 independent hexamers in complex with ssDNA and MgADP. Each is a unique biological assembly (hexamer 1: chains A-F, M, O1-6, X1-6; hexamer 2: chains G-L, N, O7-11, X7-11 ).

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Components

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DNA chain / Protein , 2 types, 14 molecules MNABCDEFGHIJKL

#1: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 3909.549 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
Replication protein E1


Mass: 31123.447 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus type 1 / Genus: Deltapapillomavirus / Species: Bovine papillomavirus - 1 / Strain: BPV-1 / Gene: E1 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03116

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Non-polymers , 4 types, 39 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2H2O11
3KCL12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 75701 / Num. obs: 74589 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7550 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite of PDB ENTRY 1TUE and unpublished structure

1tue


Resolution: 3.15→44.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 41133.91 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3626 5.1 %RANDOM
Rwork0.239 ---
obs0.239 71517 91.9 %-
all-71517 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9217 Å2 / ksol: 0.246589 e/Å3
Displacement parametersBiso mean: 74.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å25.07 Å214.02 Å2
2---10.63 Å2-2.67 Å2
3---7.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.15→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25787 262 310 15 26374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 3.15→3.29 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.431 493 5.3 %
Rwork0.388 8802 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4adp.paramadp.top
X-RAY DIFFRACTION5dna-rna_rep.paramdna-rna.top

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