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- PDB-6j5g: Complex structure of MAb 4.2-scFv with tick-borne encephalitis vi... -

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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 / nucleoside-triphosphate phosphatase / viral capsid / 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 / nucleoside-triphosphate phosphatase / viral capsid / 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 / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / 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 / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase ...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 / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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)
Has protein modificationY

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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: 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

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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

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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 )

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