[English] 日本語
Yorodumi
- PDB-7wnj: Crystal structure and Cap Binding analysis of the methyltransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wnj
TitleCrystal structure and Cap Binding analysis of the methyltransferase of Langat virus
ComponentsCore protein
KeywordsSTRUCTURAL PROTEIN / methyltransferase / Langat virus / flavivirus
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 / 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 / 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 ...RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb 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
S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesLangat virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, C. / Ruixue, L.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Structures of NS5 Methyltransferase from Zika Virus
Authors: Javier, C. / Rinku, J.
History
DepositionJan 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0972
Polymers29,7131
Non-polymers3841
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
Unit cell
Length a, b, c (Å)35.722, 91.554, 98.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 29712.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q9IG39, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% glycerol; 0.1 M Tris, pH 8.0; and 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97891 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.7→19.78 Å / Num. obs: 35880 / % possible obs: 98.8 % / Redundancy: 12.31 % / Biso Wilson estimate: 32.36 Å2 / CC1/2: 0.99 / Net I/σ(I): 25.89
Reflection shellResolution: 1.702→1.763 Å / Num. unique obs: 3143 / CC1/2: 0.89

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OXT

2oxt


Resolution: 1.7→19.78 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.59 / Phase error: 21.957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 1710 4.86 %
Rwork0.1809 33498 -
obs0.1817 35208 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 26 158 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612126
X-RAY DIFFRACTIONf_angle_d0.73692868
X-RAY DIFFRACTIONf_chiral_restr0.0508307
X-RAY DIFFRACTIONf_plane_restr0.0073370
X-RAY DIFFRACTIONf_dihedral_angle_d12.4532791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.31571320.30852397X-RAY DIFFRACTION86.23
1.75-1.810.29981530.2712825X-RAY DIFFRACTION99.8
1.81-1.870.29231410.25462823X-RAY DIFFRACTION99.7
1.87-1.950.23141450.21392816X-RAY DIFFRACTION99.73
1.95-2.040.2381440.20012814X-RAY DIFFRACTION99.33
2.04-2.140.21861470.19582839X-RAY DIFFRACTION99.14
2.14-2.280.21391530.18532797X-RAY DIFFRACTION98.4
2.28-2.450.2041230.18642804X-RAY DIFFRACTION97.76
2.45-2.70.23011160.20012820X-RAY DIFFRACTION96.87
2.7-3.090.21751350.20342812X-RAY DIFFRACTION96.72
3.09-3.890.17431460.16772867X-RAY DIFFRACTION97.76
3.89-19.780.17051750.14892884X-RAY DIFFRACTION94.47
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)
14.8487541051-1.021479272970.4891444690212.497345390281.915588425735.335466322690.0253146041756-0.7540812636520.1361949678781.395303269360.129970854045-1.20942118765-0.04720849478460.6711082541380.1113335850530.6341060555190.0145972944032-0.2140886007190.395882724578-0.09448975301390.43738551876925.06157177748.866626468129.3963218436
22.77893586530.549046591974-0.5085765135118.45385526866-2.184190522732.600373960470.122112853273-0.310943304766-0.04547041785440.9328277143360.2537761820891.2827190653-0.305089097017-0.222013620873-0.1747703982050.2992641693480.03430748294690.1081929970.3640159350240.08593308543830.4135325797949.1432733590528.406278755626.2131961742
33.80279590293-0.0341902800764-2.014983749678.70219628016-1.954424573084.72514053947-0.218204275365-0.0584624292929-0.413621761715-0.4398263467370.1717397069860.3374187977290.3859364391850.003031308236-0.04570114268570.183754740546-0.00793836983-0.03601723631260.2195995724850.06690407294170.34708787479512.58123786819.175576544720.276535285
42.47621990543-0.2886391286160.3948275627366.9318046007-2.11948147853.12950315805-0.01599101584630.201719634192-0.264190229569-1.22428509858-0.107422258395-0.6768357741310.5252013393250.1826771138840.03353526133680.3937140204620.04005234884180.108767009640.2886633461170.004135362607480.22149119545422.080915571533.14757963099.92133340602
52.170679751521.11287091481-0.3088586865448.53437652679-0.5048720451241.570461903950.06109795975910.006647566175470.1231378852270.194751478080.01924228679760.382609368289-0.111383626151-0.0332014488204-0.08140935469990.1916551609750.03596662099720.01480576622560.2662080165630.009033569648330.19005560433714.723215050544.752472057817.3464167418
62.838165742870.933623082836-0.8075320459165.95069086924-3.064919370991.281491698950.328061501805-0.41303441520.07678209306631.56713324335-0.02866707885471.34020248188-0.245142689969-0.307485226758-0.1976422308230.4261784715120.1097407455470.2067704481040.4755508208180.1034962072890.5797755238056.5302026317634.227881248429.092455734
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 28 )5 - 281 - 24
22chain 'A' and (resid 29 through 85 )29 - 8525 - 81
33chain 'A' and (resid 86 through 128 )86 - 12882 - 124
44chain 'A' and (resid 129 through 203 )129 - 203125 - 199
55chain 'A' and (resid 204 through 243 )204 - 243200 - 239
66chain 'A' and (resid 244 through 266 )244 - 266240 - 262

+
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://pdbjlvh1.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