+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43517 | |||||||||
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Title | Cryo-EM structure of HMPV (MPV-2cREKR) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Prefusion / HMPV / Cryo-EM / VIRUS / VIRAL PROTEIN | |||||||||
Function / homology | Precursor 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 species | Human metapneumovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||
Authors | Yu X / Langedijk JPM | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Efficacious human metapneumovirus vaccine based on AI-guided engineering of a closed prefusion trimer Authors: Bakkers MJG / Ritschel T / Tiemessen M / Dijkman J / Zuffiano AA / Yu X / Overveld D / Le L / Voorzaat R / Haaren M / Man M / Sharma S / Tamara S / Fits L / Zahn R / Juraszek J / Langedijk JPM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43517.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-43517-v30.xml emd-43517.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_43517.png | 39.4 KB | ||
Filedesc metadata | emd-43517.cif.gz | 5.6 KB | ||
Others | emd_43517_half_map_1.map.gz emd_43517_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43517 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43517 | HTTPS FTP |
-Validation report
Summary document | emd_43517_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_43517_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_43517_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_43517_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43517 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43517 | HTTPS FTP |
-Related structure data
Related structure data | 8vt3MC 8vt2C M: atomic model generated by this map C: citing same article (ref.) |
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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_43517.map.gz / Format: CCP4 / Size: 125 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: 0.91 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_43517_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43517_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Prefusion of HMPV (MPV-2cREKR) trimer complex
Entire | Name: Prefusion of HMPV (MPV-2cREKR) trimer complex |
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Components |
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-Supramolecule #1: Prefusion of HMPV (MPV-2cREKR) trimer complex
Supramolecule | Name: Prefusion of HMPV (MPV-2cREKR) trimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human metapneumovirus |
-Macromolecule #1: Prefusion of HMPV (MPV-2cREKR), N-fragment
Macromolecule | Name: Prefusion of HMPV (MPV-2cREKR), N-fragment / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus |
Molecular weight | Theoretical: 8.296239 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GLKESYLEES CSTITEGYLS VLRTGWYTNV FTLEVGDVEN LTCSDGPSLI KTELDLTKSA LRELKTVSAD QLARE UniProtKB: Fusion glycoprotein F0 |
-Macromolecule #2: Prefusion of HMPV (MPV-2cREKR), C-fragment
Macromolecule | Name: Prefusion of HMPV (MPV-2cREKR), C-fragment / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus |
Molecular weight | Theoretical: 41.865828 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: FVLGAIALGR ATAAAVTAGV AIAKTIRLES EVTAIKNALK TTNEAVSTLG NGVRVLATAV RELKDFVSKN LTRAINKNKC DIDDLKMAV SFSQFNRRFL NVVRQFSENA GITPAISLDL MTDAELARAI SNMPTSAGQI KLMLENRAMV RRKGFGILIG V YGSSVIYM ...String: FVLGAIALGR ATAAAVTAGV AIAKTIRLES EVTAIKNALK TTNEAVSTLG NGVRVLATAV RELKDFVSKN LTRAINKNKC DIDDLKMAV SFSQFNRRFL NVVRQFSENA GITPAISLDL MTDAELARAI SNMPTSAGQI KLMLENRAMV RRKGFGILIG V YGSSVIYM VQLPIFGVID TPCWIVKAAP SCSEKKGNYA CLLREDQGWY CQNAGSTVYY PNEKDCETRG DHVFCDTAAG IN VAEQSKE CNINISTTNY PCKVSTGRNP ISMVALSPLG ALVACYKGVS CSIGSNRVGI IKQLNKGCSY ITNQDADTVT IDN TVYQLS KVEGEQHVIK GRPVSSSFDP IKFPPDQFNV ALDQVFENIE NSQAWVRKFD EILSSIEKG UniProtKB: Fusion glycoprotein F0 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 453003 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |