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- EMDB-73493: Cryo-EM structure of the parainfluenza virus hemagglutinin-neuram... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73493
TitleCryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies 5217-2 and PIV3HN-09
Map data
Sample
  • Complex: Dimer complex of PIV3 hemagglutinin-neuraminidase with 5217-2 Fab and PIV3HN-09 Fab
    • Protein or peptide: Hemagglutinin-neuraminidase
    • Protein or peptide: PIV3HN-09 Fab HC
    • Protein or peptide: PIV3HN-09 Fab KC
    • Protein or peptide: 5217-2 Fab HC
    • Protein or peptide: 5217-2 Fab KC
Keywordsantibody / viral protein / complex / 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
DepositionOct 21, 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_73493.png

Downloads & links

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Map

FileDownload / File: emd_73493.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 408 pix.
= 359.04 Å		0.88 Å/pix.
x 408 pix.
= 359.04 Å		0.88 Å/pix.
x 408 pix.
= 359.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-1.2647889 - 1.6468071
Average (Standard dev.)-0.00006365888 (±0.02512206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 359.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73493_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73493_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73493_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 5217-2 Fab...

EntireName: Dimer complex of PIV3 hemagglutinin-neuraminidase with 5217-2 Fab and PIV3HN-09 Fab
Components
  • Complex: Dimer complex of PIV3 hemagglutinin-neuraminidase with 5217-2 Fab and PIV3HN-09 Fab
    • Protein or peptide: Hemagglutinin-neuraminidase
    • Protein or peptide: PIV3HN-09 Fab HC
    • Protein or peptide: PIV3HN-09 Fab KC
    • Protein or peptide: 5217-2 Fab HC
    • Protein or peptide: 5217-2 Fab KC

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Supramolecule #1: Dimer complex of PIV3 hemagglutinin-neuraminidase with 5217-2 Fab...

SupramoleculeName: Dimer complex of PIV3 hemagglutinin-neuraminidase with 5217-2 Fab and PIV3HN-09 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin-neuraminidase

MacromoleculeName: Hemagglutinin-neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 48.941578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QEVLPQRITH DVGIKPLNPD DFWRCTSGLP SLMKTPKIRL MPGPGLLAMP TTVDGCVRTP SLVINDLIYA YTSNLITRGC QDIGKSYQV LQIGIITVNS DLVPDLNPRI SHTFNINDNR KSCSLALLNT DVYQLCSTPK VDERSDYASS GIEDIVLDIV N YDGSISTT ...String:
QEVLPQRITH DVGIKPLNPD DFWRCTSGLP SLMKTPKIRL MPGPGLLAMP TTVDGCVRTP SLVINDLIYA YTSNLITRGC QDIGKSYQV LQIGIITVNS DLVPDLNPRI SHTFNINDNR KSCSLALLNT DVYQLCSTPK VDERSDYASS GIEDIVLDIV N YDGSISTT RFKNNNISFD QPYAALYPSV GPGIYYKGKI IFLGYGGLEH PINENVICNT TGCPGKTQRD CNQASHSPWF SD RRMVNSI IVADKGLNSI PKLKVWTISM RQNYWGSEGR LLLLGNKIYI YTRSTSWHSK LQLGIIDITD YSDIRIKWTW HNV LSRPGN NECPWGHSCP DGCITGVYTD AYPLNPTGSI VSSVILDSQK SRVNPVITYS TATERVNELA ILNRTLSAGY TTTS CITHY NKGYCFHIVE INHKSLNTFQ PMLFKTEIPK SCS

UniProtKB: Hemagglutinin-neuraminidase

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Macromolecule #2: PIV3HN-09 Fab HC

MacromoleculeName: PIV3HN-09 Fab HC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.375807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSVS SGSYYWSWIR QPPGKGLEWI GDIFTSGSTS YSPSLKSRVT ISLDGSKNHF SLKLRSVSS ADAAVYYCAR ESWEGAYLKY FDYWGQGTLV TVSS

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Macromolecule #3: PIV3HN-09 Fab KC

MacromoleculeName: PIV3HN-09 Fab KC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.727081 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPAT LSLSPGERAT LSCRASQSVS TYLAWYQQKP GQAPRLLMYD ASNRATGIPA RFSGSGSGTD FTLTISSLES EDFAVYYCQ QRSIRPWTFG QGTKVEIK

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Macromolecule #4: 5217-2 Fab HC

MacromoleculeName: 5217-2 Fab HC / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.541996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVHLLESGGG LVQPGGSRRI SCAASGFSFG SYAMSWVRQA PGKGLEWVST ITSSGESTDY ADSVKGRFII SRDNAKNTLD LLMNSLRAG DTAVYYCAKG GAVVLSAMDV WGQGTTVTVS S

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Macromolecule #5: 5217-2 Fab KC

MacromoleculeName: 5217-2 Fab KC / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.559776 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS LSASVGDRVT ITCQASHDIS NYLNWYQQKP GKAPKLLIYD ASNLETGVPP RFSGGGSGTH FSLTISSLQP EDIATYYCQ QDDSLPLTFG PGTKVEIK

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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

Concentration1.3 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
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: GATAN K3 (6k 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: 238
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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