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Yorodumi- EMDB-25929: SAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25929 | |||||||||
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Title | SAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Precursor 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 species | Homo sapiens (human) / Human metapneumovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Hsieh C-L / McLellan JS / Rush SA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25929.map.gz | 239.2 MB | EMDB map data format | |
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Header (meta data) | emd-25929-v30.xml emd-25929.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_25929.png | 49.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25929 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25929 | HTTPS FTP |
-Validation report
Summary document | emd_25929_validation.pdf.gz | 322.7 KB | Display | EMDB validaton report |
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Full document | emd_25929_full_validation.pdf.gz | 322.2 KB | Display | |
Data in XML | emd_25929_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_25929_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25929 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25929 | HTTPS FTP |
-Related structure data
Related structure data | 7tjqMC 7tl0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25929.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Complex of hMPV F with MPE8 Fab and SAN27-14 Fab
Entire | Name: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab |
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Components |
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-Supramolecule #1: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab
Supramolecule | Name: Complex of hMPV F with MPE8 Fab and SAN27-14 Fab / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SAN27-14 Fab heavy chain
Macromolecule | Name: SAN27-14 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.867521 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVRLEQSGAD VKKPGASVRV SCKASGYTFN GYYIHWVRQA PGQGLEWMGW INPYTGETNY AQTFRGRVTL TRDTSLKTLH LDLISLRSG DTAIYYCARG NCSISGCYYS WLDHWGQGTL VTVSS |
-Macromolecule #2: SAN27-14 Fab light chain
Macromolecule | Name: SAN27-14 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.546019 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPST LSASVGDRVT ITCRASQSIN TWLAWYQQKP GKAPKLLIYE ASSLERGVPS RFSGSGSGTG FTLTISSLQP DDFATYFCQ QYNTYPRTFG QGTKVEIKRT VAAPSV |
-Macromolecule #3: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus |
Molecular weight | Theoretical: 60.453852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: MPE8 Fab heavy chain
Macromolecule | Name: MPE8 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.201002 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #5: MPE8 Fab light chain
Macromolecule | Name: MPE8 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.556883 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 Details: 2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
Details | Collected 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3492 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93710 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |