+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23605 | |||||||||
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Title | Cryo-EM Structure of disulfide stabilized HMPV F v4-B | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / membrane => GO:0016020 / 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 | Human metapneumovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Gorman J / Kwong PD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Interprotomer disulfide-stabilized variants of the human metapneumovirus fusion glycoprotein induce high titer-neutralizing responses. Authors: Guillaume B E Stewart-Jones / Jason Gorman / Li Ou / Baoshan Zhang / M Gordon Joyce / Lijuan Yang / Cheng Cheng / Gwo-Yu Chuang / Kathryn E Foulds / Wing-Pui Kong / Adam S Olia / Mallika ...Authors: Guillaume B E Stewart-Jones / Jason Gorman / Li Ou / Baoshan Zhang / M Gordon Joyce / Lijuan Yang / Cheng Cheng / Gwo-Yu Chuang / Kathryn E Foulds / Wing-Pui Kong / Adam S Olia / Mallika Sastry / Chen-Hsiang Shen / John-Paul Todd / Yaroslav Tsybovsky / Raffaello Verardi / Yongping Yang / Peter L Collins / Davide Corti / Antonio Lanzavecchia / Diana G Scorpio / John R Mascola / Ursula J Buchholz / Peter D Kwong / Abstract: Human metapneumovirus (HMPV) is a major cause of respiratory disease worldwide, particularly among children and the elderly. Although there is no licensed HMPV vaccine, promising candidates have been ...Human metapneumovirus (HMPV) is a major cause of respiratory disease worldwide, particularly among children and the elderly. Although there is no licensed HMPV vaccine, promising candidates have been identified for related pneumoviruses based on the structure-based stabilization of the fusion (F) glycoprotein trimer, with prefusion-stabilized F glycoprotein trimers eliciting significantly higher neutralizing responses than their postfusion F counterparts. However, immunization with HMPV F trimers in either prefusion or postfusion conformations has been reported to elicit equivalent neutralization responses. Here we investigate the impact of stabilizing disulfides, especially interprotomer disulfides (IP-DSs) linking protomers of the F trimer, on the elicitation of HMPV-neutralizing responses. We designed F trimer disulfides, screened for their expression, and used electron microscopy (EM) to confirm their formation, including that of an unexpected postfusion variant. In mice, IP-DS-stabilized prefusion and postfusion HMPV F elicited significantly higher neutralizing responses than non-IP-DS-stabilized HMPV Fs. In macaques, the impact of IP-DS stabilization was more measured, although IP-DS-stabilized variants of either prefusion or postfusion HMPV F induced neutralizing responses many times the average titers observed in a healthy human cohort. Serological and absorption-based analyses of macaque responses revealed elicited HMPV-neutralizing responses to be absorbed differently by IP-DS-containing and by non-IP-DS-containing postfusion Fs, suggesting IP-DS stabilization to alter not only the immunogenicity of select epitopes but their antigenicity as well. We speculate the observed increase in immunogenicity by IP-DS trimers to be related to reduced interprotomer flexibility within the HMPV F trimer. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23605.map.gz | 65.6 MB | EMDB map data format | |
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Header (meta data) | emd-23605-v30.xml emd-23605.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_23605.png | 110.6 KB | ||
Masks | emd_23605_msk_1.map | 70.2 MB | Mask map | |
Others | emd_23605_additional_1.map.gz emd_23605_half_map_1.map.gz emd_23605_half_map_2.map.gz | 18.2 MB 65.1 MB 65.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23605 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23605 | HTTPS FTP |
-Validation report
Summary document | emd_23605_validation.pdf.gz | 808.6 KB | Display | EMDB validaton report |
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Full document | emd_23605_full_validation.pdf.gz | 808.1 KB | Display | |
Data in XML | emd_23605_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_23605_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23605 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23605 | HTTPS FTP |
-Related structure data
Related structure data | 7lzeMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23605.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23605_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_23605_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_23605_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_23605_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HMPV F v4-B
Entire | Name: HMPV F v4-B |
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Components |
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-Supramolecule #1: HMPV F v4-B
Supramolecule | Name: HMPV F v4-B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Human metapneumovirus |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus |
Molecular weight | Theoretical: 54.473844 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCTDCPSLIK TELDLTKSAL RELKTVSADQ LAREEQIEGG GGGGFVLGA IALGVATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIAD ...String: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCTDCPSLIK TELDLTKSAL RELKTVSADQ LAREEQIEGG GGGGFVLGA IALGVATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIAD LCMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSYMPT SAGQIKLMLE NRAMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI IKAAPSCSEK DGNYACLLRE DQGWYCKNAG STVYYPNDKD CETRGDHVFC DTA AGINVA EQSRECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLP KGCSYITNQD ADTV TIDNT VYQLSKVEGE QHVIKGRPVS SSFDPICFPE DQFNVALDQV FESIENCQAL VDQSNKILNS AESAIGGYIP EAPRD GQAY VRKDGEWVLL STFLGGLVPR |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 64.05 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |