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- EMDB-6855: JEV-2H4 Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6855
TitleJEV-2H4 Fab complex
Map data
Sample
  • Complex: JEV E protein with its mouse antibody H
    • Protein or peptide: JEV E protein
    • Protein or peptide: JEV M protein
    • Protein or peptide: 2H4 light chain
    • Protein or peptide: 2H4 heavy chain
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 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 / host cell surface / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / 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. / 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 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsQiu XD / Lei YF / Yang P / Gao Q / WANG N / Cao L / Yuan S / Wang XX / Xu ZK / Rao ZH
Funding support China, 1 items
OrganizationGrant numberCountry
National Key Research and Development Program of China2016YFC1200400 China
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural basis for neutralization of Japanese encephalitis virus by two potent therapeutic antibodies.
Authors: Xiaodi Qiu / Yingfeng Lei / Pan Yang / Qiang Gao / Nan Wang / Lei Cao / Shuai Yuan / Xiaofang Huang / Yongqiang Deng / Wenyu Ma / Tianbing Ding / Fanglin Zhang / Xingan Wu / Junjie Hu / Shan- ...Authors: Xiaodi Qiu / Yingfeng Lei / Pan Yang / Qiang Gao / Nan Wang / Lei Cao / Shuai Yuan / Xiaofang Huang / Yongqiang Deng / Wenyu Ma / Tianbing Ding / Fanglin Zhang / Xingan Wu / Junjie Hu / Shan-Lu Liu / Chengfeng Qin / Xiangxi Wang / Zhikai Xu / Zihe Rao /
Abstract: Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized . JEV is the leading causative agent of ...Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized . JEV is the leading causative agent of encephalitis, and is responsible for thousands of deaths each year in Asia. Humoral immunity is essential for protecting against flavivirus infections and passive immunization has been demonstrated to be effective in curing disease. Here, we demonstrate that JEV-specific monoclonal antibodies, 2F2 and 2H4, block attachment of the virus to its receptor and also prevent fusion of the virus. Neutralization of JEV by these antibodies is exceptionally potent and confers clear therapeutic benefit in mouse models. A single 20 μg dose of these antibodies resulted in 100% survival and complete clearance of JEV from the brains of mice. The 4.7 Å and 4.6 Å resolution cryo-electron microscopy structures of JEV-2F2-Fab and JEV-2H4-Fab complexes, together with the crystal structure of 2H4 Fab and our recent near-atomic structure of JEV , unveil the nature and location of epitopes targeted by the antibodies. Both 2F2 and 2H4 Fabs bind quaternary epitopes that span across three adjacent envelope proteins. Our results provide a structural and molecular basis for the application of 2F2 and 2H4 to treat JEV infection.
History
DepositionNov 29, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseMay 2, 2018-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ywp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6855.png

Downloads & links

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Map

FileDownload / File: emd_6855.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.03007483 - 0.087126896
Average (Standard dev.)0.0002163959 (±0.006423139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 993.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z993.600993.600993.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-0.0300.0870.000

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Supplemental data

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Sample components

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Entire : JEV E protein with its mouse antibody H

EntireName: JEV E protein with its mouse antibody H
Components
  • Complex: JEV E protein with its mouse antibody H
    • Protein or peptide: JEV E protein
    • Protein or peptide: JEV M protein
    • Protein or peptide: 2H4 light chain
    • Protein or peptide: 2H4 heavy chain

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Supramolecule #1: JEV E protein with its mouse antibody H

SupramoleculeName: JEV E protein with its mouse antibody H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Japanese encephalitis virus / Strain: P3
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)

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Macromolecule #1: JEV E protein

MacromoleculeName: JEV E protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Japanese encephalitis virus
Molecular weightTheoretical: 53.508684 KDa
SequenceString: FNCLGMGNRD FIEGASGATW VDLVLEGDSC LTIMANDKPT LDVRMINIEA SQLAEVRSYC YHASVTDIST VARCPMTGEA HNEKRADSS YVCKQGFTDR GWGNGCGLFG KGSIDTCAKF SCTSKAIGRT IQPENIKYEV GIFVHGTTTS ENHGNYSAQV G ASQAAKFT ...String:
FNCLGMGNRD FIEGASGATW VDLVLEGDSC LTIMANDKPT LDVRMINIEA SQLAEVRSYC YHASVTDIST VARCPMTGEA HNEKRADSS YVCKQGFTDR GWGNGCGLFG KGSIDTCAKF SCTSKAIGRT IQPENIKYEV GIFVHGTTTS ENHGNYSAQV G ASQAAKFT VTPNAPSITL KLGDYGEVTL DCEPRSGLNT EAFYVMTVGS KSFLVHREWF HDLALPWTPP SSTAWRNREL LM EFEEAHA TKQSVVALGS QEGGLHQALA GAIVVEYSSS VKLTSGHLKC RLKMDKLALK GTTYGMCTGK FSFAKNPADT GHG TVVIEL SYSGSDGPCK IPIVSVASLN DMTPVGRLVT VNPFVATSSA NSKVLVEMEP PFGDSYIVVG RGDKQINHHW HKAG STLGK AFLTTLKGAQ RLAALGDTAW DFGSIGGVFN SIGKAVHQVF GGAFRTLFGG MSWITQGLMG ALLLWMGVNA RDRSI ALAF LATGGVLLFL ATNVHA

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Macromolecule #2: JEV M protein

MacromoleculeName: JEV M protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Japanese encephalitis virus
Molecular weightTheoretical: 8.250488 KDa
SequenceString:
SVSVQTHGES SLVNKTETWL DSTKATRYLM KTENWIIRNP GYAFLAAVLG WMLGSNNGQR VVFTILLLLV APAY

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Macromolecule #3: 2H4 light chain

MacromoleculeName: 2H4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.840303 KDa
SequenceString: DIVLTQSPAS LAVSLGQRAT ISCRASQSVS TSYMHWYQQK PGQPPRLLIY LVSNLESGVP SRFSGSGSGT DFTLNIHPVE AEDEATYYC QHIRELTRSE AGPSWLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
DIVLTQSPAS LAVSLGQRAT ISCRASQSVS TSYMHWYQQK PGQPPRLLIY LVSNLESGVP SRFSGSGSGT DFTLNIHPVE AEDEATYYC QHIRELTRSE AGPSWLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

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Macromolecule #4: 2H4 heavy chain

MacromoleculeName: 2H4 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.337305 KDa
SequenceString: QVQLMESGPE LKKPGETVKI SCKASGYTFT DYSMHWVKQA PGKGLKWMGW INTGTGEPTF AADFKGRFAF SLETSASTAY LQINNLKNE DTASYFCARG VGLYGVDYWG QGTSVTVSSP KTTPPSVYPL APVCGDTTGS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV ...String:
QVQLMESGPE LKKPGETVKI SCKASGYTFT DYSMHWVKQA PGKGLKWMGW INTGTGEPTF AADFKGRFAF SLETSASTAY LQINNLKNE DTASYFCARG VGLYGVDYWG QGTSVTVSSP KTTPPSVYPL APVCGDTTGS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridMaterial: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 2500 / Average exposure time: 8.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 26229
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: EMAN
Final 3D classificationNumber classes: 50 / Avg.num./class: 524 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 50 / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 26229

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