[English] 日本語
Yorodumi
- PDB-6j5g: Complex structure of MAb 4.2-scFv with tick-borne encephalitis vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j5g
TitleComplex structure of MAb 4.2-scFv with tick-borne encephalitis virus envelope protein
Components
  • Envelope protein E
  • antibody heavy chain
  • antibody light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / protective and neutralizing antibody / flavivirus envelope protein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / 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 / : / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain ...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 / : / 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 / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesTick-borne encephalitis virus European subtype
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.291 Å
AuthorsYang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Tien, P. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2019
Title: Molecular Basis of a Protective/Neutralizing Monoclonal Antibody Targeting Envelope Proteins of both Tick-Borne Encephalitis Virus and Louping Ill Virus.
Authors: Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Gao, G.F. / Tien, P.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 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
A: Envelope protein E
H: antibody heavy chain
L: antibody light chain


Theoretical massNumber of molelcules
Total (without water)69,7653
Polymers69,7653
Non-polymers00
Water00
1
A: Envelope protein E
H: antibody heavy chain
L: antibody light chain

A: Envelope protein E
H: antibody heavy chain
L: antibody light chain


Theoretical massNumber of molelcules
Total (without water)139,5316
Polymers139,5316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Unit cell
Length a, b, c (Å)135.731, 100.693, 140.236
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Envelope protein E


Mass: 44618.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus European subtype (strain Neudoerfl)
Strain: Neudoerfl
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P14336
#2: Antibody antibody heavy chain


Mass: 13169.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody antibody light chain


Mass: 11977.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.84 Å3/Da / Density % sol: 82.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 5, 5% PGA-LM, 8% PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 28405 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 105.68 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.259 / Net I/σ(I): 36.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.499 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 2816 / CC1/2: 0.577 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVB, 5GRJ

1svb

5grj


Resolution: 3.291→46 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1135 4.99 %
Rwork0.2077 --
obs0.2084 22756 80.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.291→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 0 0 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134691
X-RAY DIFFRACTIONf_angle_d1.5026371
X-RAY DIFFRACTIONf_dihedral_angle_d13.3921685
X-RAY DIFFRACTIONf_chiral_restr0.07701
X-RAY DIFFRACTIONf_plane_restr0.011815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2909-3.44060.3156320.3056678X-RAY DIFFRACTION20
3.4406-3.6220.3265910.26661505X-RAY DIFFRACTION45
3.622-3.84880.27151390.24372686X-RAY DIFFRACTION80
3.8488-4.14580.21341570.22553303X-RAY DIFFRACTION99
4.1458-4.56260.16961910.17393332X-RAY DIFFRACTION100
4.5626-5.22210.18831810.16923371X-RAY DIFFRACTION100
5.2221-6.57620.22351720.20553356X-RAY DIFFRACTION99
6.5762-46.00450.24271720.21813390X-RAY DIFFRACTION98
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)
11.3977-0.26050.59251.69050.58390.8936-0.6610.08650.5254-0.63070.1739-0.49130.22920.550.27281.5728-0.21020.1582.30690.06171.3817-25.21411.8581183.8827
20.29760.14950.39450.1453-0.48052.06770.1096-1.0135-0.2580.04410.35050.06750.4475-1.4682-0.26021.2521-0.0491-0.10742.46110.11330.675-37.6536-4.7459145.3119
33.10960.15350.5423.88790.62514.34130.12170.43790.0721-0.30370.21860.1458-0.2607-0.2695-0.16590.28260.1006-0.01790.27780.06050.4184-5.30832.9681191.1938
41.5926-0.0299-0.47763.40993.43293.6307-0.0305-0.4708-0.21410.62580.05030.65510.2661-0.1535-0.10760.55210.04760.07510.2235-0.0310.5342-3.7002-30.5217214.3401
55.05470.4892.00752.5743-1.68813.1141-0.05390.6532-0.13420.0035-0.15640.2134-0.08470.19820.12050.2343-0.03290.02530.1478-0.00670.3155-0.3814-22.1572206.1576
64.5306-1.3019-1.43794.95690.55376.42520.04380.1988-0.0148-0.37010.41120.99290.0931-0.41540.01480.1896-0.0405-0.00080.2107-0.0590.5854-6.8495-26.3826205.0394
72.90671.25070.38764.4994-1.54712.4237-0.0017-0.1766-0.1581-0.08070.19660.0946-0.1491-0.2245-0.1880.28620.04960.03770.2046-0.00830.36312.2775-27.297208.6222
85.7093-6.10694.99646.8963-5.15994.7828-0.00070.8966-1.0996-0.1175-0.2564-0.0310.56390.31130.0390.27620.20650.00890.4214-0.05240.481916.1719-19.4301197.2658
94.9599-1.0993-1.44354.2995-1.7758.1720.0108-0.56610.3076-0.18670.0027-1.31450.25931.1221-0.09930.30370.0203-0.02860.35610.02610.806130.4309-23.7309212.97
105.7143-4.72155.97215.821-5.57316.45480.03190.35480.1286-0.31950.10340.3315-0.29610.2074-0.17860.24610.020.0840.21940.04350.486723.4995-16.9764203.4469
110.64630.3915-0.34641.15940.29520.9444-0.0310.22640.1256-0.2990.05730.03080.1555-0.19790.33050.5042-0.1765-0.1219-0.04040.01570.719913.8817-13.7649204.7453
124.7604-2.6258-2.13231.8024-0.36967.7909-0.2513-1.0071-1.2590.4358-0.15380.38860.45190.43690.12130.3101-0.0377-0.03570.29960.04430.56313.2227-24.4792215.6462
134.4943-3.18310.53028.7145-4.79793.0975-0.3103-0.50790.78670.73710.3526-0.0351-1.04340.3121-0.0270.4236-0.1135-0.04480.2824-0.04150.527117.6171-10.734214.5761
146.3644-3.83245.82187.7352-6.55977.1355-0.6268-0.36180.58350.77270.0608-0.2556-0.9617-0.38320.52410.25080.01620.04760.2759-0.06310.45224.1277-17.241213.0732
152.6121-1.66680.97642.2833-1.63311.18310.4306-0.27330.3588-0.4049-0.4378-0.4470.45740.0635-0.11470.3077-0.09310.0410.172-0.07660.477810.6909-18.1688202.7971
165.0694-4.67623.78716.4639-0.98256.83810.32760.0418-2.1280.2926-0.57620.00131.18971.1273-0.10370.4177-0.0554-0.09540.43550.22810.662327.1506-28.6054212.4318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 397 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 28 )
5X-RAY DIFFRACTION5chain 'H' and (resid 29 through 60 )
6X-RAY DIFFRACTION6chain 'H' and (resid 61 through 83 )
7X-RAY DIFFRACTION7chain 'H' and (resid 84 through 120 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 7 )
9X-RAY DIFFRACTION9chain 'L' and (resid 8 through 18 )
10X-RAY DIFFRACTION10chain 'L' and (resid 19 through 25 )
11X-RAY DIFFRACTION11chain 'L' and (resid 26 through 38 )
12X-RAY DIFFRACTION12chain 'L' and (resid 39 through 48 )
13X-RAY DIFFRACTION13chain 'L' and (resid 49 through 67 )
14X-RAY DIFFRACTION14chain 'L' and (resid 68 through 83 )
15X-RAY DIFFRACTION15chain 'L' and (resid 84 through 102 )
16X-RAY DIFFRACTION16chain 'L' and (resid 103 through 108 )

+
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