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- EMDB-73975: Cryo-EM structure of the parainfluenza virus hemagglutinin-neuram... -

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Basic information

Entry
Database: EMDB / ID: EMD-73975
TitleCryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies PIV3HN-05 and PIV3HN-13
Map data
Sample
  • Complex: Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 Fab and PIV3HN-13 Fab
    • Protein or peptide: Hemagglutinin-neuraminidase
    • Protein or peptide: PIV3HN-13 heavy chain
    • Protein or peptide: PIV3HN-13 light chain
    • Protein or peptide: PIV3HN-05 heavy chain
    • Protein or peptide: PIV3HN-05 light chain
  • Ligand: alpha-L-fucopyranose
Keywordsantibody / viral protein / complex / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHomo sapiens (human) / Human respirovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsMcCaffrey KD / Mousa JJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI181850-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143865 United States
CitationJournal: To Be Published
Title: Structural Insights into HN-Targeted Monoclonal Antibodies against Human Parainfluenza Virus Type 3
Authors: McCaffrey KD / Mousa JJ
History
DepositionNov 20, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73975.png

Downloads & links

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Map

FileDownload / File: emd_73975.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 306.88 Å		1.1 Å/pix.
x 280 pix.
= 306.88 Å		1.1 Å/pix.
x 280 pix.
= 306.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.281
Minimum - Maximum-1.9536958 - 3.0003288
Average (Standard dev.)0.0035534545 (±0.05627285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 306.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73975_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73975_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73975_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 ...

EntireName: Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 Fab and PIV3HN-13 Fab
Components
  • Complex: Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 Fab and PIV3HN-13 Fab
    • Protein or peptide: Hemagglutinin-neuraminidase
    • Protein or peptide: PIV3HN-13 heavy chain
    • Protein or peptide: PIV3HN-13 light chain
    • Protein or peptide: PIV3HN-05 heavy chain
    • Protein or peptide: PIV3HN-05 light chain
  • Ligand: alpha-L-fucopyranose

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Supramolecule #1: Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 ...

SupramoleculeName: Dimer complex of PIV3 hemagglutinin-neuraminidase with PIV3HN-05 Fab and PIV3HN-13 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#5, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: PIV3HN-05 heavy chain

MacromoleculeName: PIV3HN-05 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.359586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG VVQPGGSLRL SCVASGLSLS PNWMHWVRQA PGKGLVWVSR ISDNGDTTNY AGSVMGRFTI SRDNAKNTLY LQMNNLRAD DTAVYFCVRE SAVISSPSWG LYDTAYHFDP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EVQLVESGGG VVQPGGSLRL SCVASGLSLS PNWMHWVRQA PGKGLVWVSR ISDNGDTTNY AGSVMGRFTI SRDNAKNTLY LQMNNLRAD DTAVYFCVRE SAVISSPSWG LYDTAYHFDP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCDKTHT CP PCPAPEL LG

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Macromolecule #2: PIV3HN-05 light chain

MacromoleculeName: PIV3HN-05 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.87715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SGTPGQGVTI SCSGSNSNIG TNAVDWYQQF PGTAPRLLIF NDNQRPSGVP DRFSGSRSGT SASLAISGLQ SEDEAVYYC ATWDDSLNGP VVFGGGTKLT VLRQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSA SGTPGQGVTI SCSGSNSNIG TNAVDWYQQF PGTAPRLLIF NDNQRPSGVP DRFSGSRSGT SASLAISGLQ SEDEAVYYC ATWDDSLNGP VVFGGGTKLT VLRQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #3: Hemagglutinin-neuraminidase

MacromoleculeName: Hemagglutinin-neuraminidase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 51.625516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHSLVP RGSISEITIR NDNQEVLPQR ITHDVGIKPL NPDDFWRCTS GLPSLMKTPK IRLMPGPGLL AMPTTVDGCV RTPSLVIND LIYAYTSNLI TRGCQDIGKS YQVLQIGIIT VNSDLVPDLN PRISHTFNIN DNRKSCSLAL LNTDVYQLCS T PKVDERSD ...String:
HHHHHHSLVP RGSISEITIR NDNQEVLPQR ITHDVGIKPL NPDDFWRCTS GLPSLMKTPK IRLMPGPGLL AMPTTVDGCV RTPSLVIND LIYAYTSNLI TRGCQDIGKS YQVLQIGIIT VNSDLVPDLN PRISHTFNIN DNRKSCSLAL LNTDVYQLCS T PKVDERSD YASSGIEDIV LDIVNYDGSI STTRFKNNNI SFDQPYAALY PSVGPGIYYK GKIIFLGYGG LEHPINENVI CN TTGCPGK TQRDCNQASH SPWFSDRRMV NSIIVADKGL NSIPKLKVWT ISMRQNYWGS EGRLLLLGNK IYIYTRSTSW HSK LQLGII DITDYSDIRI KWTWHNVLSR PGNNECPWGH SCPDGCITGV YTDAYPLNPT GSIVSSVILD SQKSRVNPVI TYST ATERV NELAILNRTL SAGYTTTSCI THYNKGYCFH IVEINHKSLN TFQPMLFKTE IPKSCS

UniProtKB: Hemagglutinin-neuraminidase

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Macromolecule #4: PIV3HN-13 heavy chain

MacromoleculeName: PIV3HN-13 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.32127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGA LVQPGGSLRV SCAASGFSFS SYAMSWLRQT PGKGLEWVSA IGGSGHSTYY ADSVQGRFTV SRDNSKDTLY LQMNSLRAE DTAVYYCAKF FRSDGVFHFD YWGPGNPGSP SPASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLLESGGA LVQPGGSLRV SCAASGFSFS SYAMSWLRQT PGKGLEWVSA IGGSGHSTYY ADSVQGRFTV SRDNSKDTLY LQMNSLRAE DTAVYYCAKF FRSDGVFHFD YWGPGNPGSP SPASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH TCPPCPAPEL LG

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Macromolecule #5: PIV3HN-13 light chain

MacromoleculeName: PIV3HN-13 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.785422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPLS LPVTPGEPAS ISCRSSQSLR HSDGNNYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGSDFTLKI SRVEAEDVG VYYCMQALQT PTFGQGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLR HSDGNNYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGSDFTLKI SRVEAEDVG VYYCMQALQT PTFGQGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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Macromolecule #7: alpha-L-fucopyranose

MacromoleculeName: alpha-L-fucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: FUC
Molecular weightTheoretical: 164.156 Da
Chemical component information

ChemComp-FUC:
alpha-L-fucopyranose

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: Phosphate Buffered Saline
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 343
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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