[English] 日本語
Yorodumi
- PDB-7nxu: Crystal structure of the tick-borne encephalitis virus NS3 helica... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nxu
TitleCrystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP-Pi
ComponentsNS3 helicase domain
KeywordsVIRAL PROTEIN / RNA helicase / hydrolase / flavivirus
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAnindita, P.D. / Grinkevich, P. / Franta, Z.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Mechanistic insight into the RNA-stimulated ATPase activity of tick-borne encephalitis virus helicase.
Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z.
#1: Journal: Biorxiv / Year: 2022
Title: Mechanistic insight into the ATP hydrolysis cycle of tick-borne encephalitis virus helicase
Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z.
History
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Sep 14, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS3 helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0895
Polymers53,4891
Non-polymers6004
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-32 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.980, 72.980, 196.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NS3 helicase domain / Serine protease NS3


Mass: 53489.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A0A2S1PWV0, RNA helicase

-
Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis Tris Propane, 0.02 M Sodium potassium phosphate pH 7.5, 20% w/v, PEG 3350 10% v/v, Ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.097→48.81 Å / Num. obs: 31603 / % possible obs: 99.5 % / Redundancy: 13.67 % / CC1/2: 0.99 / Net I/σ(I): 23.02
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 3.21 / Num. unique obs: 5033 / CC1/2: 0.904 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BM0

7bm0


Resolution: 2.1→48.806 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2507 1547 4.896 %
Rwork0.2138 30047 -
all0.216 --
obs-31594 98.396 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.072 Å2-0 Å2-0 Å2
2--1.072 Å2-0 Å2
3----2.144 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 1 200 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133462
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173208
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6534693
X-RAY DIFFRACTIONr_angle_other_deg2.3631.5867370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91420.503199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9131536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023897
X-RAY DIFFRACTIONr_gen_planes_other0.010.02826
X-RAY DIFFRACTIONr_nbd_refined0.2040.2626
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.22950
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21630
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.28
X-RAY DIFFRACTIONr_nbd_other0.3230.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.26
X-RAY DIFFRACTIONr_mcbond_it3.5653.8871704
X-RAY DIFFRACTIONr_mcbond_other3.563.8851703
X-RAY DIFFRACTIONr_mcangle_it5.1115.8182123
X-RAY DIFFRACTIONr_mcangle_other5.115.822124
X-RAY DIFFRACTIONr_scbond_it4.364.4161758
X-RAY DIFFRACTIONr_scbond_other4.3564.4151758
X-RAY DIFFRACTIONr_scangle_it6.7626.452570
X-RAY DIFFRACTIONr_scangle_other6.7616.4592571
X-RAY DIFFRACTIONr_lrange_it7.87344.8433763
X-RAY DIFFRACTIONr_lrange_other7.9544.7733746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1520.3291090.2892207X-RAY DIFFRACTION99.2288
2.152-2.210.3111190.2732135X-RAY DIFFRACTION100
2.21-2.2750.535880.4981678X-RAY DIFFRACTION80.3823
2.275-2.3450.2571050.2492041X-RAY DIFFRACTION99.814
2.345-2.4210.245910.2091980X-RAY DIFFRACTION100
2.421-2.5060.3021020.2121937X-RAY DIFFRACTION100
2.506-2.6010.247930.2091851X-RAY DIFFRACTION100
2.601-2.7070.286940.2421769X-RAY DIFFRACTION98.5714
2.707-2.8280.263780.211709X-RAY DIFFRACTION100
2.828-2.9650.253800.2031659X-RAY DIFFRACTION100
2.965-3.1260.246780.221589X-RAY DIFFRACTION100
3.126-3.3150.23980.231485X-RAY DIFFRACTION100
3.315-3.5440.236860.231377X-RAY DIFFRACTION98.8514
3.544-3.8280.238560.1981332X-RAY DIFFRACTION99.7843
3.828-4.1930.217600.1751212X-RAY DIFFRACTION99.375
4.193-4.6880.192550.1571117X-RAY DIFFRACTION100
4.688-5.4130.217460.1671006X-RAY DIFFRACTION100
5.413-6.6280.231450.19862X-RAY DIFFRACTION99.8899
6.628-9.3680.201400.169686X-RAY DIFFRACTION100

+
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