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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of HMPV (MPV-2cREKR) | |||||||||
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![]() | Prefusion / HMPV / Cryo-EM / VIRUS / VIRAL PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
![]() | Yu X / Langedijk JPM | |||||||||
Funding support | 1 items
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![]() | ![]() 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 | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
Images | ![]() | 53.5 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.948 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43516_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43516_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Prefusion of HMPV (MPV-2cREKR)
Entire | Name: Prefusion of HMPV (MPV-2cREKR) |
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Components |
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-Supramolecule #1: Prefusion of HMPV (MPV-2cREKR)
Supramolecule | Name: Prefusion of HMPV (MPV-2cREKR) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Prefusion of HMPV (MPV-2c)
Macromolecule | Name: Prefusion of HMPV (MPV-2c) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.553586 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC SDGPSLIKTE LDLTKSALRE LKTVSADQL RRRRELPRFM NYTLNNAKKT NVTLSKKRKR RFVLGAIALG RATAAAVTAG VAIAKTIRLE SEVTAIKNAL K TTNEAVST ...String: MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC SDGPSLIKTE LDLTKSALRE LKTVSADQL RRRRELPRFM NYTLNNAKKT NVTLSKKRKR RFVLGAIALG RATAAAVTAG VAIAKTIRLE SEVTAIKNAL K TTNEAVST LGNGVRVLAT AVRELKDFVS KNLTRAINKN KCDIDDLKMA VSFSQFNRRF LNVVRQFSEN AGITPAISLD LM TDAELAR AISNMPTSAG QIKLMLENRA MVRRKGFGIL IGVYGSSVIY MVQLPIFGVI DTPCWIVKAA PSCSEKKGNY ACL LREDQG WYCQNAGSTV YYPNEKDCET RGDHVFCDTA AGINVAEQSK ECNINISTTN YPCKVSTGRN PISMVALSPL GALV ACYKG VSCSIGSNRV GIIKQLNKGC SYITNQDADT VTIDNTVYQL SKVEGEQHVI KGRPVSSSFD PIKFPPDQFN VALDQ VFEN IENSQAWVRK FDEILSSIEK GNTGGSEPEA |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97386 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |