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- EMDB-25929: SAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-25929
TitleSAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F
Map data
Sample
  • Complex: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab
    • Protein or peptide: SAN27-14 Fab heavy chain
    • Protein or peptide: SAN27-14 Fab light chain
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPE8 Fab heavy chain
    • Protein or peptide: MPE8 Fab light chain
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human) / Human metapneumovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsHsieh C-L / McLellan JS / Rush SA
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: Cell Rep / Year: 2022
Title: Characterization of prefusion-F-specific antibodies elicited by natural infection with human metapneumovirus.
Authors: Scott A Rush / Gurpreet Brar / Ching-Lin Hsieh / Emilie Chautard / Jennifer N Rainho-Tomko / Chris D Slade / Christine A Bricault / Ana Kume / James Kearns / Rachel Groppo / Sophia T Mundle ...Authors: Scott A Rush / Gurpreet Brar / Ching-Lin Hsieh / Emilie Chautard / Jennifer N Rainho-Tomko / Chris D Slade / Christine A Bricault / Ana Kume / James Kearns / Rachel Groppo / Sophia T Mundle / Linong Zhang / Danilo Casimiro / Tong-Ming Fu / Joshua M DiNapoli / Jason S McLellan /
Abstract: Human metapneumovirus (hMPV) is a major cause of acute respiratory infections in infants and older adults, for which no vaccines or therapeutics are available. The viral fusion (F) glycoprotein is ...Human metapneumovirus (hMPV) is a major cause of acute respiratory infections in infants and older adults, for which no vaccines or therapeutics are available. The viral fusion (F) glycoprotein is required for entry and is the primary target of neutralizing antibodies; however, little is known about the humoral immune response generated from natural infection. Here, using prefusion-stabilized F proteins to interrogate memory B cells from two older adults, we obtain over 700 paired non-IgM antibody sequences representing 563 clonotypes, indicative of a highly polyclonal response. Characterization of 136 monoclonal antibodies reveals broad recognition of the protein surface, with potently neutralizing antibodies targeting each antigenic site. Cryo-EM studies further reveal two non-canonical sites and the molecular basis for recognition of the apex of hMPV F by two prefusion-specific neutralizing antibodies. Collectively, these results provide insight into the humoral response to hMPV infection in older adults and will help guide vaccine development.
History
DepositionJan 16, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25929.png

Downloads & links

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Map

FileDownload / File: emd_25929.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.81 Å/pix.
x 432 pix.
= 349.92 Å		0.81 Å/pix.
x 432 pix.
= 349.92 Å		0.81 Å/pix.
x 432 pix.
= 349.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.02
Minimum - Maximum-5.3341527 - 85.28992
Average (Standard dev.)2.5574266e-07 (±0.9999925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 349.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of hMPV F with MPE8 Fab and SAN27-14 Fab

EntireName: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab
Components
  • Complex: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab
    • Protein or peptide: SAN27-14 Fab heavy chain
    • Protein or peptide: SAN27-14 Fab light chain
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPE8 Fab heavy chain
    • Protein or peptide: MPE8 Fab light chain

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Supramolecule #1: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab

SupramoleculeName: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SAN27-14 Fab heavy chain

MacromoleculeName: SAN27-14 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.867521 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVRLEQSGAD VKKPGASVRV SCKASGYTFN GYYIHWVRQA PGQGLEWMGW INPYTGETNY AQTFRGRVTL TRDTSLKTLH LDLISLRSG DTAIYYCARG NCSISGCYYS WLDHWGQGTL VTVSS

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Macromolecule #2: SAN27-14 Fab light chain

MacromoleculeName: SAN27-14 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.546019 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQSIN TWLAWYQQKP GKAPKLLIYE ASSLERGVPS RFSGSGSGTG FTLTISSLQP DDFATYFCQ QYNTYPRTFG QGTKVEIKRT VAAPSV

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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 metapneumovirus
Molecular weightTheoretical: 60.453852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTVSADQL AREEQIENPR RRRFVLGAIA CGVATAAAVT AGVAIAKCIR LESEVTAIKN CLKKTNECVS TLGCGVRVLA T AVRELKDF ...String:
MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTVSADQL AREEQIENPR RRRFVLGAIA CGVATAAAVT AGVAIAKCIR LESEVTAIKN CLKKTNECVS TLGCGVRVLA T AVRELKDF VSKNLTRAIN KNKCDIPDLK MAVSFSQFNR RFLNVVRQFS DNAGITPAIS KDLMTDAELA RAISNMPTSA GQ IKLMLEN RAMVRRKGFG ILIGVYGSSV IYMVQLPIFG VIDTPCWIVK AAPSCSEKKG NYACLLREDQ GWYCQNAGST VYY PCEKDC ETRGDHVFCD TAAGINVAEQ SKECNINIST TNYPCKVSCG RHPISMVALS PLGALVACYK GVSCSIGSNR VGII KQLNK GCSYITNQDA DTVTIDNTVY QLSKVEGEQH VIKGRPVSSS FDPVKFPQDQ FNVALDQCFE SIENSQALVD QSNRI LSSA EKGNTGGGGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEK

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Macromolecule #4: MPE8 Fab heavy chain

MacromoleculeName: MPE8 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.201002 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASGFTFS SYSMNWVRQA PGKGLEWVSS ISASSSYSDY ADSAKGRFTI SRDNAKTSLF LQMNSLRAE DTAIYFCARA RATGYSSITP YFDIWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVESGGG LVKPGGSLRL SCAASGFTFS SYSMNWVRQA PGKGLEWVSS ISASSSYSDY ADSAKGRFTI SRDNAKTSLF LQMNSLRAE DTAIYFCARA RATGYSSITP YFDIWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD QS

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Macromolecule #5: MPE8 Fab light chain

MacromoleculeName: MPE8 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.556883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VVTQPPSVSG APGQRVTISC TGSSSNIGAG YDVHWYQQLP GTAPKLLIYD NNNRPSGVPD RFSASKSGTS ASLAITGLQA EDEADYYCQ SYDRSLSGVF GTGTKVTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
VVTQPPSVSG APGQRVTISC TGSSSNIGAG YDVHWYQQLP GTAPKLLIYD NNNRPSGVPD RFSASKSGTS ASLAITGLQA EDEADYYCQ SYDRSLSGVF GTGTKVTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHKSYSCQVT HEGSTVEKTV APTECS

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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

Concentration0.5 mg/mL
BufferpH: 8
Details: 2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE
DetailsCollected on tilt, CF-1.2-1.3 grids with 0.5 mg/mL DSCavEs2 (2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol) and 2x fold molar excess MPE8 and 1.5x fold molar excess SAN27-14 spiked in ~10 minutes before freezing. 3 u of sample was deposited and the grid was plunge frozen using a Vitrobot Mark IV using 4 seconds blot time and -2 force at 100% humidity and 10 C

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3492 / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93710

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