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- PDB-4e2i: The Complex Structure of the SV40 Helicase Large T Antigen and p6... -

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Basic information

Entry
Database: PDB / ID: 4e2i
TitleThe Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase
Components
  • DNA polymerase alpha subunit BDNA polymerase
  • Large T antigenLarge tumor antigen
KeywordsHydrolase/DNA binding Protein / replication initiation / Hydrolase-DNA binding complex / Hydrolase-DNA binding Protein complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / bidirectional double-stranded viral DNA replication ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication initiation / Activation of the pre-replicative complex / helicase activity / Defective pyroptosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein import into nucleus / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / DNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Large T antigen, polyomaviridae / DNA polymerase alpha, subunit B, N-terminal domain superfamily / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily ...Large T antigen, polyomaviridae / DNA polymerase alpha, subunit B, N-terminal domain superfamily / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Large T antigen / DNA polymerase alpha subunit B / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsZhou, B. / Arnett, D.R. / Yu, X. / Brewster, A. / Sowd, G.A. / Xie, C.L. / Vila, S. / Gai, D. / Fanning, E. / Chen, X.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for the interaction of a hexameric replicative helicase with the regulatory subunit of human DNA polymerase alpha-primase.
Authors: Zhou, B. / Arnett, D.R. / Yu, X. / Brewster, A. / Sowd, G.A. / Xie, C.L. / Vila, S. / Gai, D. / Fanning, E. / Chen, X.S.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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
A: Large T antigen
B: Large T antigen
C: Large T antigen
D: Large T antigen
E: Large T antigen
F: Large T antigen
G: Large T antigen
H: Large T antigen
I: Large T antigen
J: Large T antigen
K: Large T antigen
L: Large T antigen
2: DNA polymerase alpha subunit B
3: DNA polymerase alpha subunit B
6: DNA polymerase alpha subunit B
U: DNA polymerase alpha subunit B
W: DNA polymerase alpha subunit B
5: DNA polymerase alpha subunit B
7: DNA polymerase alpha subunit B
9: DNA polymerase alpha subunit B
1: DNA polymerase alpha subunit B
4: DNA polymerase alpha subunit B
8: DNA polymerase alpha subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,24735
Polymers597,46223
Non-polymers78512
Water0
1
A: Large T antigen
B: Large T antigen
C: Large T antigen
D: Large T antigen
E: Large T antigen
F: Large T antigen
2: DNA polymerase alpha subunit B
3: DNA polymerase alpha subunit B
6: DNA polymerase alpha subunit B
5: DNA polymerase alpha subunit B
1: DNA polymerase alpha subunit B
4: DNA polymerase alpha subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,47418
Polymers303,08112
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Large T antigen
H: Large T antigen
I: Large T antigen
J: Large T antigen
K: Large T antigen
L: Large T antigen
U: DNA polymerase alpha subunit B
W: DNA polymerase alpha subunit B
7: DNA polymerase alpha subunit B
9: DNA polymerase alpha subunit B
8: DNA polymerase alpha subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,77317
Polymers294,38011
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26740 Å2
ΔGint-90 kcal/mol
Surface area80780 Å2
Unit cell
Length a, b, c (Å)249.098, 249.098, 387.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Large T antigen / Large tumor antigen


Mass: 41812.664 Da / Num. of mol.: 12 / Fragment: UNP residues 266-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DH70, UniProt: P03070*PLUS
#2: Protein
DNA polymerase alpha subunit B / DNA polymerase / DNA polymerase alpha 70 kDa subunit


Mass: 8700.879 Da / Num. of mol.: 11 / Fragment: UNP residues 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14181
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 5.02 Å3/Da / Density % sol: 75.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.96 M sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 5→50 Å / Num. all: 53345 / Num. obs: 39723 / % possible obs: 74.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 5→5.18 Å / % possible all: 78.5

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Processing

Software
NameClassification
HKL-2000data collection
CCP4model building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3139 3538 Random
Rwork0.3047 --
obs0.3047 35234 -
all-53345 -
Refinement stepCycle: LAST / Resolution: 5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41862 0 12 0 41874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002597
X-RAY DIFFRACTIONc_angle_d0.65442

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