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- EMDB-41505: Hemagglutinin-neuraminidase from Human parainfluenza virus type 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-41505
TitleHemagglutinin-neuraminidase from Human parainfluenza virus type 3: complex with rPIV3-23 and rPIV3-28 Fabs
Map dataDeepEMhancer output map
Sample
  • Complex: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs
    • Complex: Hemagglutinin-neuraminidase glycoprotein
      • Protein or peptide: Hemagglutinin-neuraminidase
    • Complex: Recombinant rPIV3-28 Fab
      • Protein or peptide: Heavy chain Fab rPIV3-28
      • Protein or peptide: Light chain Fab rPIV3-28
    • Complex: Recombinant rPIV3-23 Fab
      • Protein or peptide: Heavy chain Fab rPIV3-23
      • Protein or peptide: Light chain Fab rPIV3-23
KeywordsImmune system / viral neutralization / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman respirovirus 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41505.png

Downloads & links

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Map

FileDownload / File: emd_41505.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer output map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.58
Minimum - Maximum-0.0018039957 - 2.1765883
Average (Standard dev.)0.0017939326 (±0.031820916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41505_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_41505_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 HN in complex with rPIV3-23 and rPIV3-28 Fabs

EntireName: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs
Components
  • Complex: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs
    • Complex: Hemagglutinin-neuraminidase glycoprotein
      • Protein or peptide: Hemagglutinin-neuraminidase
    • Complex: Recombinant rPIV3-28 Fab
      • Protein or peptide: Heavy chain Fab rPIV3-28
      • Protein or peptide: Light chain Fab rPIV3-28
    • Complex: Recombinant rPIV3-23 Fab
      • Protein or peptide: Heavy chain Fab rPIV3-23
      • Protein or peptide: Light chain Fab rPIV3-23

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Supramolecule #1: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs

SupramoleculeName: HPIV3 HN in complex with rPIV3-23 and rPIV3-28 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respirovirus 3

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Supramolecule #2: Hemagglutinin-neuraminidase glycoprotein

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

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Supramolecule #3: Recombinant rPIV3-28 Fab

SupramoleculeName: Recombinant rPIV3-28 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Recombinant rPIV3-23 Fab

SupramoleculeName: Recombinant rPIV3-23 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
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: 50.774414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVPPQRITHD VGIKPLNPDD FWRCTSGLPS LMKTPKIRLM PGPGLLAMPT TVDGCVRTPS LVINDLIYAY TSNLITRGCQ DIGKSYQVL QIGIITVNSD LVPDLNPRIS HTFNINDNRK SCSLALLNTD VYQLCSTPKV DERSDYASSG IEDIVLDIVN H DGSISTTR ...String:
EVPPQRITHD VGIKPLNPDD FWRCTSGLPS LMKTPKIRLM PGPGLLAMPT TVDGCVRTPS LVINDLIYAY TSNLITRGCQ DIGKSYQVL QIGIITVNSD LVPDLNPRIS HTFNINDNRK SCSLALLNTD VYQLCSTPKV DERSDYASSG IEDIVLDIVN H DGSISTTR FKNNNISFDQ PYAALYPSVG PGIYYKGKII FLGYGGLEHP INENAICNTT GCPGKTQRDC NQASHSPWFS DR RMVNSII VVDKGLNSIP KLKVWTISMR QNYWGSEGRL LLLGNKIYIY TRSTSWHSKL QLGIIDITDY SDIRIKWTWH NVL SRPGNN ECPWGHSCPD GCITGVYTDA YPLNPTGSIV SSVILDSQKS RVNPVITYST STERVNELAI RNKTLSAGYT TTSC ITHYN KGYCFHIVEI NHKSLDTFQP MLFKTEIPKS CSGSENLYFQ GGSHHHHHH

UniProtKB: Hemagglutinin-neuraminidase

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Macromolecule #2: Heavy chain Fab rPIV3-28

MacromoleculeName: Heavy chain Fab rPIV3-28 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.344152 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVKLLESGGG LIQPGDSLRL SCAASGFTFS TFAMSWVRQA PGKGLEWVSV ITSTGSSADY ADSVKGRFTM SRDNSKNTVY LQMDSLRAD DTAVYFCAKQ GATILSSFES WGQGSLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVKLLESGGG LIQPGDSLRL SCAASGFTFS TFAMSWVRQA PGKGLEWVSV ITSTGSSADY ADSVKGRFTM SRDNSKNTVY LQMDSLRAD DTAVYFCAKQ GATILSSFES WGQGSLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #3: Light chain Fab rPIV3-28

MacromoleculeName: Light chain Fab rPIV3-28 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.592119 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASIGDRVT ITCQASQDID KYLNWYQQKP GKAPKLLIYD ASNFETGVPS RFSGSGSGTY FTFTISSLQA EDIATYYCQ QYDDLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASIGDRVT ITCQASQDID KYLNWYQQKP GKAPKLLIYD ASNFETGVPS RFSGSGSGTY FTFTISSLQA EDIATYYCQ QYDDLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLRSPVTKS FNRGEC

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Macromolecule #4: Heavy chain Fab rPIV3-23

MacromoleculeName: Heavy chain Fab rPIV3-23 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.95298 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQESGPG LVRPSQTLSL TCSVSGASIT DDLNRWSWIR QHPGKGLECV GYISYSGTTY YNPSLQGRLS ISLDTSRNQV SLKLTSVTA ADTAVYFCAR APIIMSSPSW GLYDQDYVPM DVWGQGTTVF VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVQLQESGPG LVRPSQTLSL TCSVSGASIT DDLNRWSWIR QHPGKGLECV GYISYSGTTY YNPSLQGRLS ISLDTSRNQV SLKLTSVTA ADTAVYFCAR APIIMSSPSW GLYDQDYVPM DVWGQGTTVF VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Macromolecule #5: Light chain Fab rPIV3-23

MacromoleculeName: Light chain Fab rPIV3-23 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.309943 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVMTQSPAT LSVSPGERVT LSCRASQSVG SDLAWYQQKP GQAPRLLIYG ASTRATGVPA KFSGSGSGTE FTLTISGLQS EDFALYYCH QYNNWWTFGL GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIVMTQSPAT LSVSPGERVT LSCRASQSVG SDLAWYQQKP GQAPRLLIYG ASTRATGVPA KFSGSGSGTE FTLTISGLQS EDFALYYCH QYNNWWTFGL GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLRSPVTKSF NRGEC

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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

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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 / Cs: 2.7 mm / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47827
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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