[English] 日本語
Yorodumi
- PDB-2ntc: Crystal Structure of sv40 large T antigen origin binding domain w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ntc
TitleCrystal Structure of sv40 large T antigen origin binding domain with DNA
Components
  • (21-nt PEN element of the SV40 DNA origin) x 2
  • large T antigenLarge tumor antigen
KeywordsDNA binding protein/DNA / origin binding domain / protein-DNA complex / replication / DNA binding protein-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / 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 ...Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / 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 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Large T antigen / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBohm, A. / Meinke, G. / Bullock, P.A.
CitationJournal: Plos Biol. / Year: 2007
Title: The Crystal Structure of the SV40 T-Antigen Origin Binding Domain in Complex with DNA
Authors: Meinke, G. / Phelan, P. / Moine, S. / Bochkareva, E. / Bochkarev, A. / Bullock, P.A. / Bohm, A.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
W: 21-nt PEN element of the SV40 DNA origin
C: 21-nt PEN element of the SV40 DNA origin
A: large T antigen
B: large T antigen


Theoretical massNumber of molelcules
Total (without water)43,7184
Polymers43,7184
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.489, 68.341, 97.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe asymmetric unit contains two t-antigen origin binding domain molecules bound to a dna target that contains two high affinity binding sites

-
Components

#1: DNA chain 21-nt PEN element of the SV40 DNA origin


Mass: 6415.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 21-nt PEN element of the SV40 DNA origin


Mass: 6473.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein large T antigen / Large tumor antigen


Mass: 15414.633 Da / Num. of mol.: 2 / Fragment: Origin binding domain (residues 131-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Strain: 776 / Gene: large T antigen / Plasmid: pGEX-1lT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03070, UniProt: Q98ZP7*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.1 M calcium acetate, 30 % v/v peg 8000, 20 % glycerol, VAPOR DIFFUSION, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2calcium acetate11
3peg 800011
4glycerol11
5sodium cacodylate12
6calcium acetate12
7peg 800012
8glycerol12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2005 / Details: crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 15755 / Num. obs: 15314 / % possible obs: 90.1 % / Observed criterion σ(I): 2.1 / Redundancy: 12.2 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 2.1

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: t antigen origin binding domain and four base pairs duplex dna

Resolution: 2.4→38.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.329 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.523 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28692 772 4.9 %RANDOM
Rwork0.2049 ---
all0.2088 15755 --
obs0.2088 14921 90.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---4.37 Å20 Å2
3---5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 855 0 77 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213079
X-RAY DIFFRACTIONr_angle_refined_deg2.0132.2994343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0125251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09923.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6211510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022041
X-RAY DIFFRACTIONr_nbd_refined0.2390.21239
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4590.23
X-RAY DIFFRACTIONr_mcbond_it0.8781.51299
X-RAY DIFFRACTIONr_mcangle_it1.57522055
X-RAY DIFFRACTIONr_scbond_it1.86832295
X-RAY DIFFRACTIONr_scangle_it2.8664.52288
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 29 -
Rwork0.297 706 -
obs--58.33 %
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)
18.39833.35125.67219.91593.59619.7363-0.088-0.265-0.933-0.15930.67710.94471.0058-0.1001-0.5891-0.2066-0.05080.03150.05030.07740.2779-9.261-29.1451.976
26.867-4.03742.28047.24871.30112.1889-0.2292-0.52191.07030.7454-0.3025-1.2936-0.93270.13390.5317-0.08750.0462-0.14490.0495-0.0010.543722.96525.5329.598
31.1212-0.86820.02610.3252-0.09370.33350.09390.0082-0.1424-0.8168-0.1762-0.0307-0.00250.00340.0823-0.0638-0.00260.0385-0.2667-0.03880.112411.791-2.972-17.801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC233 - 258105 - 130
2X-RAY DIFFRACTION2BD233 - 258105 - 130
3X-RAY DIFFRACTION3WA2 - 212 - 21
4X-RAY DIFFRACTION3CB23 - 431 - 21

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more