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- EMDB-41506: Human parainfluenza virus type 3 prefusion F trimer in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-41506
TitleHuman parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab
Map data
Sample
  • Complex: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab
    • Complex: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: rPIV3-18 light chain
      • Protein or peptide: Light chain Fab rPIV3-28
    • Complex: rPIV3-18 heavy chain
      • Protein or peptide: Heavy chain Fab rPIV3-18
KeywordsImmune system / viral neutralization / VIRAL PROTEIN
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman respirovirus 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOtrelo-Cardoso AR / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI13752 United States
CitationJournal: Nat Microbiol / Year: 2024
Title: Functional and structural basis of human parainfluenza virus type 3 neutralization with human monoclonal antibodies.
Authors: Naveenchandra Suryadevara / Ana Rita Otrelo-Cardoso / Nurgun Kose / Yao-Xiong Hu / Elad Binshtein / Rachael M Wolters / Alexander L Greninger / Laura S Handal / Robert H Carnahan / Anne ...Authors: Naveenchandra Suryadevara / Ana Rita Otrelo-Cardoso / Nurgun Kose / Yao-Xiong Hu / Elad Binshtein / Rachael M Wolters / Alexander L Greninger / Laura S Handal / Robert H Carnahan / Anne Moscona / Theodore S Jardetzky / James E Crowe /
Abstract: Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have ...Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have been approved yet. The haemagglutinin-neuraminidase (HN) and fusion (F) surface glycoproteins of hPIV3 are major antigenic determinants. Here we describe naturally occurring potently neutralizing human antibodies directed against both surface glycoproteins of hPIV3. We isolated seven neutralizing HN-reactive antibodies and a pre-fusion conformation F-reactive antibody from human memory B cells. One HN-binding monoclonal antibody (mAb), designated PIV3-23, exhibited functional attributes including haemagglutination and neuraminidase inhibition. We also delineated the structural basis of neutralization for two HN and one F mAbs. MAbs that neutralized hPIV3 in vitro protected against infection and disease in vivo in a cotton rat model of hPIV3 infection, suggesting correlates of protection for hPIV3 and the potential clinical utility of these mAbs.
History
DepositionAug 7, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41506.png

Downloads & links

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Map

FileDownload / File: emd_41506.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.49912775 - 1.2670485
Average (Standard dev.)0.0014102409 (±0.050778687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41506_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_41506_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 : HPIV3 prefusion F trimer in complex with rPIV3-18 Fab

EntireName: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab
Components
  • Complex: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab
    • Complex: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: rPIV3-18 light chain
      • Protein or peptide: Light chain Fab rPIV3-28
    • Complex: rPIV3-18 heavy chain
      • Protein or peptide: Heavy chain Fab rPIV3-18

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Supramolecule #1: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab

SupramoleculeName: HPIV3 prefusion F trimer in complex with rPIV3-18 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respirovirus 3

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Supramolecule #2: Fusion glycoprotein F0

SupramoleculeName: Fusion glycoprotein F0 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human respirovirus 3

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Supramolecule #3: rPIV3-18 light chain

SupramoleculeName: rPIV3-18 light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: rPIV3-18 heavy chain

SupramoleculeName: rPIV3-18 heavy chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Heavy chain Fab rPIV3-18

MacromoleculeName: Heavy chain Fab rPIV3-18 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.959973 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLLESGGG LVRPGGSLRL SCAASGFTFS KYVMAWVRQA PGKGLEWVSS ITSGERTFYA DSVKGRFTVS RDNSKYTLDL EMSRLRAED TAVYYCAKMF KWDYDTSDFG VWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLLESGGG LVRPGGSLRL SCAASGFTFS KYVMAWVRQA PGKGLEWVSS ITSGERTFYA DSVKGRFTVS RDNSKYTLDL EMSRLRAED TAVYYCAKMF KWDYDTSDFG VWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

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Macromolecule #2: Light chain Fab rPIV3-28

MacromoleculeName: Light chain Fab rPIV3-28 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.671273 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DFQMTQSPST LSASVGDRVT ITCRASQSVG NWLTWYQHKP GKAPKILIYK ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QFNTYSWTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DFQMTQSPST LSASVGDRVT ITCRASQSVG NWLTWYQHKP GKAPKILIYK ASTLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QFNTYSWTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLRSPVTKS FNRGEC

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Macromolecule #3: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 57.360102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLKL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQAKSDIEKL KEAIRDTNKA VQSVCSSVGN CIVAIKSVQD Y VNKEIVPS ...String:
QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLKL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQAKSDIEKL KEAIRDTNKA VQSVCSSVGN CIVAIKSVQD Y VNKEIVPS IARLGCEAAG LQLGIALTQH YSELTNCFGD NIGSLQEKGI KLQCIASLYR TNITEIFTTS TVDKYDIYDL LF TESIKVR VIDVDLNDYS ITLQVRLPLL TRLLNTQIYK VDSISYNIQN REWYIPLPSH IMTKGAFLGG ADVKECIEAF SSY ICPSDP GFVLNHEMES CLSGNISQCP RTTVTSDIVP RYAFVNGGVV ANCITTTCTC NGIGNRINQP PDQGVKIITH KECN TIGIN GMLFNTNKEG TLAFYTPDDI TLNNSVALDP IDISIELNKV KSDLEESKEW YRRSNQKLSA IEDKIEEILS KIYHI ENEI ARIKKLIGEA PGSENLYFQG GSGSHHHHHH HH

UniProtKB: Fusion glycoprotein F0

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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

Concentration1.15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 278016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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