[English] 日本語
Yorodumi
- PDB-5yvv: Crystal structure of full length NS3 protein (gD4NS2BNS3) from DE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yvv
TitleCrystal structure of full length NS3 protein (gD4NS2BNS3) from DENV4 in closed conformation
Components(Genome polyprotein) x 2
KeywordsVIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / ATPASE / DENGUE VIRUS / FLAVIVIRUS
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / P-loop containing nucleotide triphosphate hydrolases / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.097 Å
AuthorsPHOO, W.W. / Sahili, A.E.
Funding support Singapore, 4items
OrganizationGrant numberCountry
NTUSTART UP GRANT Singapore
NMRCCBRG14MAY051 Singapore
NMRCCBRG/0103/2016 Singapore
NRFCRP001-063 Singapore
CitationJournal: To Be Published
Title: Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain
Authors: Phoo, W.W. / Sahili, A.E. / Zhang, Z.Z. / Chen, M.W. / Lescar, J. / Vasudevan, S. / Luo, D.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Genome polyprotein
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)73,2932
Polymers73,2932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-20 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.917, 88.715, 81.295
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Genome polyprotein


Mass: 67548.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1494-2092 / Mutation: L30S,F31S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4, UniProt: Q2YHF0*PLUS
#2: Protein Genome polyprotein


Mass: 5745.130 Da / Num. of mol.: 1 / Fragment: UNP residues 1393-1439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4, UniProt: Q2YHF0*PLUS
Sequence detailsThe structure is split in two chains due to the fact that one chain comes for the cofactor and the ...The structure is split in two chains due to the fact that one chain comes for the cofactor and the other from the NS3 protein.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.5, 12% PEG6000 / PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.41 Å / Num. obs: 13710 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.07 / Rrim(I) all: 0.106 / Net I/σ(I): 13.1
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2433 / CC1/2: 0.824 / Rpim(I) all: 0.375 / Rrim(I) all: 0.554 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vbc

2vbc


Resolution: 3.097→45.414 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 583 4.26 %random selection
Rwork0.2333 ---
obs0.2352 13693 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.097→45.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 0 0 4776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034877
X-RAY DIFFRACTIONf_angle_d0.6516628
X-RAY DIFFRACTIONf_dihedral_angle_d10.8461773
X-RAY DIFFRACTIONf_chiral_restr0.024743
X-RAY DIFFRACTIONf_plane_restr0.003868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0968-3.40830.34951530.32023190X-RAY DIFFRACTION98
3.4083-3.90120.32451400.26523281X-RAY DIFFRACTION100
3.9012-4.91420.271470.2113297X-RAY DIFFRACTION100
4.9142-45.4190.23961430.20883342X-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)
11.07-1.28530.78420.9746-0.26251.6384-0.4039-0.39060.1129-0.06940.15250.147-0.2264-0.13260.28981.2717-0.0199-0.3160.86140.03861.05267.349817.9644128.8457
25.0826-0.6507-1.21365.22771.3984.2420.1949-0.35620.02540.3213-0.72470.4549-0.0998-0.5150.38770.3115-0.05040.10510.4169-0.10770.397738.253823.465398.7503
32.94880.11151.79662.83661.94693.86840.3778-0.2861-0.0563-0.2108-0.2903-0.11820.1549-0.4007-0.10980.3952-0.04070.09540.36660.04310.3650.184110.224383.2594
42.14713.3692-0.09925.86580.29660.36650.1097-0.2269-0.42060.4232-0.52091.05580.2818-1.52170.5261.05830.20490.13431.80520.2911.464156.54795.4369127.5572
50.14240.6216-0.81192.7703-3.62174.787-0.87040.38080.33250.92990.30720.694-0.28850.16960.46331.5795-0.1533-0.08451.04050.16081.555157.429213.9889137.6337
60.9878-1.5092-1.44883.9201-1.20299.4043-0.7668-0.1690.67470.50970.30390.9006-0.7108-0.03190.55341.66580.2573-0.24241.2414-0.26261.746864.356925.4506143.131
70.2862-0.74320.55424.52131.24143.8646-0.91590.53480.716-0.54830.35420.3096-0.69490.91840.36270.76120.1618-0.34511.4601-0.13030.818278.335622.3951142.7754
89.3768-6.5398-5.68136.76973.72033.46620.71191.6131-0.7241-2.2942-0.35581.4779-1.49-0.8936-0.11351.9537-0.4183-0.85541.13430.22281.552785.476719.8137122.7417
90.51470.7621-0.31953.69751.6041.87450.7615-0.1504-0.8865-1.052-1.36970.33270.20020.68880.582.3346-0.256-0.1881.16490.18481.746783.933214.8757120.0143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 20 through 180 )
2X-RAY DIFFRACTION2chain 'B' and (resid 181 through 324 )
3X-RAY DIFFRACTION3chain 'B' and (resid 325 through 618 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 58 )
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 63 )
7X-RAY DIFFRACTION7chain 'A' and (resid 64 through 73 )
8X-RAY DIFFRACTION8chain 'A' and (resid 74 through 78 )
9X-RAY DIFFRACTION9chain 'A' and (resid 79 through 88 )

+
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