[English] 日本語
Yorodumi
- PDB-4lif: Crystal structure of the JCV large T-antigen origin binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lif
TitleCrystal structure of the JCV large T-antigen origin binding domain
ComponentsLarge T antigen
KeywordsHydrolase / dna binding protein / origin binding domain / replication / polyomavirus
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / DNA replication / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / DNA replication / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / zinc ion binding / ATP binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Large T antigen, polyomaviridae / 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 / Replication Protein E1; Chain: A, / Large T antigen, polyomaviridae / 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
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMeinke, G. / Bohm, A. / Bullock, P.
CitationJournal: Plos Pathog. / Year: 2014
Title: Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain.
Authors: Meinke, G. / Phelan, P.J. / Kalekar, R. / Shin, J. / Archambault, J. / Bohm, A. / Bullock, P.A.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3633
Polymers15,1701
Non-polymers1922
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.793, 103.793, 34.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Large T antigen / LT / LT-AG


Mass: 15170.390 Da / Num. of mol.: 1 / Fragment: OBD (unp residues 132-261)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Gene: Large T antigen / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M LiSO4, 30 % Peg 4000, VAPOR DIFFUSION, SITTING DROP, temperature 273K, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 5909 / Num. obs: 5906 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 37.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUF

2fuf


Resolution: 2.6→36.696 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.39 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 267 4.59 %RANDOM
Rwork0.1759 ---
obs0.1782 11188 99.79 %-
all-5639 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→36.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 10 5 1046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071072
X-RAY DIFFRACTIONf_angle_d0.991447
X-RAY DIFFRACTIONf_dihedral_angle_d14.231380
X-RAY DIFFRACTIONf_chiral_restr0.067154
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5987-2.86020.32941160.28152654X-RAY DIFFRACTION99
2.8602-3.27380.32171330.24442682X-RAY DIFFRACTION100
3.2738-4.12380.26471310.18662661X-RAY DIFFRACTION100
4.1238-36.70.16771340.14082677X-RAY DIFFRACTION100
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)
16.1909-2.1312-1.32217.1521-0.30863.62240.0871-0.39370.0234-0.23230.0711-0.6461-0.0621-0.0498-0.00020.51480.06470.02040.4959-0.0250.455411.7118-10.96154.7417
20.5112-0.3418-0.01440.41120.58411.71850.38941.08280.7163-0.65620.1446-0.736-0.95570.45740.00330.91130.06890.22520.7535-0.00910.871516.1259-3.0035-6.1407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 133:224)
2X-RAY DIFFRACTION2(chain A and resid 225:259)

+
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