[English] 日本語
Yorodumi
- PDB-4fg0: Structure of the St. Louis Encephalitis Virus envelope protein in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fg0
TitleStructure of the St. Louis Encephalitis Virus envelope protein in the fusogenic trimer conformation.
ComponentsPolyproteinProteolysis
KeywordsVIRAL PROTEIN / Viral envelope proteins / structural genomics / fusion peptide / antibody epitopes / Flavivirus / St. Louis Encephalitis Virus / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Envelope protein E
Similarity search - Component
Biological speciesSt. Louis encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.899 Å
AuthorsLuca, V.C. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Virol. / Year: 2013
Title: Structure of the st. Louis encephalitis virus postfusion envelope trimer.
Authors: Luca, V.C. / Nelson, C.A. / Fremont, D.H.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyprotein


Theoretical massNumber of molelcules
Total (without water)44,6141
Polymers44,6141
Non-polymers00
Water0
1
A: Polyprotein

A: Polyprotein

A: Polyprotein


Theoretical massNumber of molelcules
Total (without water)133,8423
Polymers133,8423
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area12620 Å2
ΔGint3 kcal/mol
Surface area49420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.485, 177.485, 177.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein Polyprotein / Proteolysis


Mass: 44613.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) St. Louis encephalitis virus / Strain: St. Louis Encephalitis Virus, strain MS1-7 / Gene: Envelope protein E / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9ENF3, UniProt: P09732*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.44 %
Crystal growTemperature: 293 K / Method: hanging drop, vapor diffusion / pH: 5.5
Details: 3% PEG 8000, 2% ethylene glycol, 0.1M Acetate pH 5.5, hanging drop, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionRedundancy: 22.1 % / Av σ(I) over netI: 30.36 / Number: 191328 / Rmerge(I) obs: 0.11 / Χ2: 1.02 / D res high: 3.9 Å / D res low: 35 Å / Num. obs: 8657 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.373510010.0581.09820.9
6.668.3710010.0821.05521.3
5.826.6610010.1191.0121.9
5.295.8210010.1171.03422.2
4.915.2910010.1221.08722.3
4.624.9110010.1291.00522.5
4.394.6210010.2021.00222.5
4.24.3910010.2660.98322.5
4.044.210010.4330.9522.5
3.94.0410010.7330.96522.6
ReflectionResolution: 3.899→35 Å / Num. obs: 8657 / % possible obs: 100 % / Redundancy: 22.1 % / Rmerge(I) obs: 0.11 / Χ2: 1.019 / Net I/σ(I): 30.36
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2
3.9-4.0422.60.7336.218800.965
4.04-4.222.50.4338330.95
4.2-4.3922.50.2668570.983
4.39-4.6222.50.2028471.002
4.62-4.9122.50.1298651.005
4.91-5.2922.30.1228601.087
5.29-5.8222.20.1178561.034
5.82-6.6621.90.1198721.01
6.66-8.3721.30.0828701.055
8.37-3520.90.0589171.098

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.03 Å37.81 Å
Translation4.03 Å37.81 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.899→34.808 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8137 / SU ML: 1.01 / σ(F): 0 / Phase error: 25.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2666 847 9.9 %
Rwork0.2218 --
obs0.2262 8555 98.87 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.227 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 367.26 Å2 / Biso mean: 152.6137 Å2 / Biso min: 63.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.899→34.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 0 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023013
X-RAY DIFFRACTIONf_angle_d0.524088
X-RAY DIFFRACTIONf_chiral_restr0.036470
X-RAY DIFFRACTIONf_plane_restr0.002524
X-RAY DIFFRACTIONf_dihedral_angle_d9.0331073
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.899-4.1430.33261320.28471228136095
4.143-4.46230.25431380.20581273141199
4.4623-4.91030.20861410.17712711412100
4.9103-5.61820.23111420.183512941436100
5.6182-7.06870.25021390.218812961435100
7.0687-34.8090.30241550.249113461501100
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)
12.3584-0.9469-1.53151.42931.16972.81930.0254-0.61150.5720.58360.3001-0.0303-0.46570.4299-0.37460.58670.13850.24230.332-0.17810.307-24.911136.61845.4372
22.442-2.8912-2.86543.51393.22594.8842-0.09920.0967-0.08220.618-0.18290.3002-0.0024-0.4520.10790.53460.11350.22520.69430.00760.1843-27.624334.419447.1536
31.2605-0.0279-0.85134.4567-0.3153.2991-0.1994-0.7513-0.76781.30750.11120.31510.19660.37380.16220.81160.23370.15530.7570.33931.0054-20.59844.542141.6806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:179)A2 - 179
2X-RAY DIFFRACTION2chain 'A' and (resseq 180:293)A180 - 293
3X-RAY DIFFRACTION3chain 'A' and (resseq 294:404)A294 - 404

+
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