[English] 日本語
Yorodumi
- PDB-5j4v: The crystal structure of Inhibitor Bound to JCV Helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j4v
TitleThe crystal structure of Inhibitor Bound to JCV Helicase
ComponentsLarge T antigenLarge tumor antigen
KeywordsHYDROLASE/INHIBITOR / Helicase / hexamer / Zn / ATP / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / metal ion binding
Similarity search - Function
Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / 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 ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6JH / Large T antigen
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å
AuthorsTer Haar, E.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors.
Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / ...Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / Rijnbrand, R. / Taylor, W.P. / Wilson, D. / Zhou, Y. / Zwahlen, J. / Ter Haar, E.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0515
Polymers42,3891
Non-polymers6624
Water88349
1
A: Large T antigen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)258,30630
Polymers254,3346
Non-polymers3,97224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area16270 Å2
ΔGint-175 kcal/mol
Surface area91190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.920, 109.920, 66.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 42388.984 Da / Num. of mol.: 1 / Fragment: UNP residues 261-628
Mutation: E280A, D295N, N299A, Q301A, Q302A, K304A, K305A, E307A, K308A, K309A, I354L, D408E, R624A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli (E. coli)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

-
Non-polymers , 5 types, 53 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6JH / 2-(2-phenoxypyridin-3-yl)[1,3]thiazolo[5,4-c]pyridine


Mass: 305.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11N3OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.75 Å3/Da / Density % sol: 55.28 % / Description: hexagonal button
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25-30% Peg400, 0.1 M LiSO4, 0.1M HEPES (pH 7.0), 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.936→54.96 Å / Num. obs: 9135 / % possible obs: 91.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 62.09 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.936-2.9466.10.3661100
13.56-54.964.60.022189.6

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.94→54.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.414
RfactorNum. reflection% reflectionSelection details
Rfree0.247 455 5 %RANDOM
Rwork0.165 ---
obs0.169 9102 91.4 %-
Displacement parametersBiso max: 156.93 Å2 / Biso mean: 61.64 Å2 / Biso min: 15.52 Å2
Baniso -1Baniso -2Baniso -3
1-7.4655 Å20 Å20 Å2
2--7.4655 Å20 Å2
3----14.9309 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.94→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 53 49 2943
Biso mean--68.02 42.22 -
Num. residues----358
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1033SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes447HARMONIC5
X-RAY DIFFRACTIONt_it2954HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3594SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2954HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4008HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion20.71
LS refinement shellResolution: 2.94→3.29 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.301 137 5.02 %
Rwork0.174 2591 -
all-2728 -
obs--97.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.46141.77720.78815.42240.64462.09890.14130.1866-0.0164-0.1601-0.08950.40260.0023-0.0972-0.0518-0.22690.024-0.0036-0.16970.08110.1968-23.89547.0867-12.8277
23.06990.5667-0.52811.3531-0.25081.02440.1823-0.2246-0.11680.0763-0.1241-0.2542-0.00740.1421-0.0582-0.2462-0.0283-0.0016-0.26810.07220.2592-31.804419.288315.3772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A1
2X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A266 - 356
3X-RAY DIFFRACTION2{ A|357 - A|512 A|518 - A|628 }A357 - 512
4X-RAY DIFFRACTION2{ A|357 - A|512 A|518 - A|628 }A518 - 628

+
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