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- EMDB-48850: CryoEM structure of WNV (Kunjin strain) with the Fab of WNV-86 an... -

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Basic information

Entry
Database: EMDB / ID: EMD-48850
TitleCryoEM structure of WNV (Kunjin strain) with the Fab of WNV-86 antibody
Map dataLocalized reconstruction of one asymmetric unit
Sample
  • Virus: West Nile virus (Kunjin)
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Small envelope protein M
    • Protein or peptide: WNV-86 heavy chain
    • Protein or peptide: WNV-86 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / 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 / Immunoglobulin E-set / helicase superfamily c-terminal domain / 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
Biological speciesKunjin virus / Homo sapiens (human) / West Nile virus (Kunjin)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKhare B / Klose T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Embo Rep. / Year: 2026
Title: A distinct E dimer epitope underlies selective recognition by a protective human West Nile virus antibody
Authors: Khare B / Arnaud CA / Klose T / Rossmann MG / Crowe JE / Kuhn RJ
History
DepositionJan 30, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48850.png

Downloads & links

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Map

FileReleased
AnnotationLocalized reconstruction of one asymmetric unit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 164 pix.
= 283.72 Å		1.73 Å/pix.
x 164 pix.
= 283.72 Å		1.73 Å/pix.
x 164 pix.
= 283.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.144
Minimum - Maximum-1.2724463 - 2.213085
Average (Standard dev.)0.01864997 (±0.0981853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 283.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full icosahedrally averaged virus map

Fileemd_48850_additional_1.map
AnnotationFull icosahedrally averaged virus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48850_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48850_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : West Nile virus (Kunjin)

EntireName: West Nile virus (Kunjin)
Components
  • Virus: West Nile virus (Kunjin)
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Small envelope protein M
    • Protein or peptide: WNV-86 heavy chain
    • Protein or peptide: WNV-86 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: West Nile virus (Kunjin)

SupramoleculeName: West Nile virus (Kunjin) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 11078 / Sci species name: West Nile virus (Kunjin) / Sci species strain: Kunjin virus (STRAIN MRM61C) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aves (birds)
Virus shellShell ID: 1 / Name: E and M / Diameter: 460.0 Å / T number (triangulation number): 3

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Macromolecule #1: Envelope protein E

MacromoleculeName: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Kunjin virus
Molecular weightTheoretical: 53.714086 KDa
Recombinant expressionOrganism: Aedes albopictus C6/36 cell densovirus
SequenceString: FNCLGMSNRD FLEGVSGATW VDLVLEGDSC VTIMSKDKPT IDVKMMNMEA ANLAEVRSYC YLATVSELST KAACPTMGEA HNDKRADPS FVCKQGVVDR GWGNGCGLFG KGSIDTCAKF ACSTKATGRT ILKENIKYEV AIFVHGPTTV ESHGNYFTQT G AAQAGRFS ...String:
FNCLGMSNRD FLEGVSGATW VDLVLEGDSC VTIMSKDKPT IDVKMMNMEA ANLAEVRSYC YLATVSELST KAACPTMGEA HNDKRADPS FVCKQGVVDR GWGNGCGLFG KGSIDTCAKF ACSTKATGRT ILKENIKYEV AIFVHGPTTV ESHGNYFTQT G AAQAGRFS ITPAAPSYTL KLGEYGEVTV DCEPRSGIDT SAYYVMTVGT KTFLVHREWF MDLNLPWSSA ESNVWRNRET LM EFEEPHA TKQSVIALGS QEGALHQALA GAIPVEFSSN TVKLTSGHLK CRVKMEKLQL KGTTYGVCSK AFRFLGTPAD TGH GTVVLE LQYTGTDGPC KIPISSVASL NDLTPVGRLV TVNPFVSVST ANAKVLIELE PPFGDSYIVV GRGEQQINHH WHKS GSSIG KAFTATLKGA QRLAALGDTA WDFGSVGGVF TSVGKAVHQV FGGAFRSLFG GMSWITQGLL GALLLWMGIN ARDRS IALT FLAVGGVLLF LSVNVH

UniProtKB: Genome polyprotein

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Macromolecule #2: Small envelope protein M

MacromoleculeName: Small envelope protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Kunjin virus
Molecular weightTheoretical: 8.221576 KDa
Recombinant expressionOrganism: Aedes albopictus C6/36 cell densovirus
SequenceString:
SLTVQTHGES TLSNKKGAWM DSTKATRYLV KTESWILRNP GYALVAAVIG WMLGSNTMQR VVFAVLLLLV APAYS

UniProtKB: Genome polyprotein

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Macromolecule #3: WNV-86 heavy chain

MacromoleculeName: WNV-86 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.623166 KDa
SequenceString:
EVQLVESGGG LVQPGRSLRL CCAASGFSFD DFAMHWVRQA PGKGLEWVSG INWNSGHIGY ADSVKGRFTI SRDNAKNSLC LQMNSLRPE DTALYYCAKD RAYYFGSGTS GGAFDVWGQG TLVTVSS

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Macromolecule #4: WNV-86 light chain

MacromoleculeName: WNV-86 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.549895 KDa
SequenceString:
DIVMTQSPSS LSASVGDRVT ITCRASQNII SYLNWYQQKP GKAPKLLIYD ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ RSFSTPLTFG GGTKVEIK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8 / Details: 10 mM Tris pH 8.0, 120 mM NaCl, 1 mM EDTA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 12760
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9n3b:
CryoEM structure of WNV (Kunjin strain) with the Fab of WNV-86 antibody

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