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- PDB-7bm0: Crystal structure of the tick-borne encephalitis virus NS3 helica... -

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Basic information

Entry
Database: PDB / ID: 7bm0
TitleCrystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP
ComponentsNS3 helicase domain
KeywordsVIRAL PROTEIN / RNA helicase / hydrolase
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Genome polyprotein
Similarity search - Component
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 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 1.4Oct 12, 2022Group: Database references / Refinement description
Category: citation / pdbx_refine_tls / pdbx_refine_tls_group
Item: _citation.journal_id_ISSN
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0734
Polymers53,4891
Non-polymers5843
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-15 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.952, 72.952, 196.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#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: pET-19b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Codonplus-RIPL / References: UniProt: A0A2S1PWV0, RNA helicase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis Tris Propane pH 6.5, 0.02 M sodium potassium phosphate pH. 7.5, 20% w/v PEG 3350, 10% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→45.71 Å / Num. obs: 43006 / % possible obs: 99.9 % / Redundancy: 14.25 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.64 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 6796 / CC1/2: 0.795 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AY4

7ay4
PDB Unreleased entry


Resolution: 1.9→45.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.261 / ESU R Free: 0.129 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2294 959 2.23 %
Rwork0.2162 42047 -
all0.217 --
obs-43006 99.916 %
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: 42.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.679 Å20 Å20 Å2
2--0.679 Å2-0 Å2
3----1.357 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 33 230 3632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123496
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6524740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28920.243206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43515585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2631539
X-RAY DIFFRACTIONr_chiral_restr0.0790.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022671
X-RAY DIFFRACTIONr_nbd_refined0.2060.21588
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.210
X-RAY DIFFRACTIONr_mcbond_it03.9791714
X-RAY DIFFRACTIONr_mcangle_it05.9452139
X-RAY DIFFRACTIONr_scbond_it04.4651782
X-RAY DIFFRACTIONr_scangle_it06.5162601
X-RAY DIFFRACTIONr_lrange_it054.6275299
X-RAY DIFFRACTIONr_rigid_bond_restr7.21433496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9460.277690.2773024X-RAY DIFFRACTION99.2937
1.946-1.9990.3680.2872967X-RAY DIFFRACTION100
1.999-2.0570.296660.2562910X-RAY DIFFRACTION100
2.057-2.1210.257640.2482808X-RAY DIFFRACTION100
2.121-2.190.251620.2372734X-RAY DIFFRACTION100
2.19-2.2670.227610.2272651X-RAY DIFFRACTION100
2.267-2.3530.211590.2112582X-RAY DIFFRACTION100
2.353-2.4490.231560.2282457X-RAY DIFFRACTION100
2.449-2.5570.225530.2242350X-RAY DIFFRACTION100
2.557-2.6820.264530.2242302X-RAY DIFFRACTION100
2.682-2.8270.202490.2022146X-RAY DIFFRACTION99.9545
2.827-2.9990.178470.1782075X-RAY DIFFRACTION100
2.999-3.2060.314440.2411935X-RAY DIFFRACTION100
3.206-3.4630.238420.2341829X-RAY DIFFRACTION100
3.463-3.7930.307380.2111670X-RAY DIFFRACTION99.9415
3.793-4.240.186350.1861542X-RAY DIFFRACTION100
4.24-4.8960.153310.1531380X-RAY DIFFRACTION100
4.896-5.9960.201270.1871178X-RAY DIFFRACTION100
5.996-8.4750.181220.181939X-RAY DIFFRACTION100
8.475-45.710.304130.227568X-RAY DIFFRACTION98.6418
Refinement TLS params.Method: refined / Origin x: -17.4382 Å / Origin y: 28.8647 Å / Origin z: -14.4455 Å
111213212223313233
T0.0577 Å20.0067 Å20.0302 Å2-0.0237 Å2-0.0054 Å2--0.0318 Å2
L0.6096 °2-0.1397 °2-0.1539 °2-1.0509 °2-0.2691 °2--1.8829 °2
S-0.0068 Å °0.0559 Å °-0.0976 Å °-0.2348 Å °-0.0435 Å °-0.1053 Å °0.1266 Å °0.1109 Å °0.0504 Å °

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