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- EMDB-43516: Cryo-EM structure of HMPV (MPV-2cREKR) -

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Basic information

Entry
Database: EMDB / ID: EMD-43516
TitleCryo-EM structure of HMPV (MPV-2cREKR)
Map data
Sample
  • Complex: Prefusion of HMPV (MPV-2cREKR)
    • Protein or peptide: Prefusion of HMPV (MPV-2c)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPrefusion / HMPV / Cryo-EM / VIRUS / VIRAL PROTEIN
Biological speciesHuman metapneumovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsYu X / Langedijk JPM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionJan 25, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43516.png

Downloads & links

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Map

FileDownload / File: emd_43516.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 242.688 Å		0.95 Å/pix.
x 256 pix.
= 242.688 Å		0.95 Å/pix.
x 256 pix.
= 242.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.948 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.3594687 - 1.963642
Average (Standard dev.)0.0006632078 (±0.0545859)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 242.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43516_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43516_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prefusion of HMPV (MPV-2cREKR)

EntireName: Prefusion of HMPV (MPV-2cREKR)
Components
  • Complex: Prefusion of HMPV (MPV-2cREKR)
    • Protein or peptide: Prefusion of HMPV (MPV-2c)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Prefusion of HMPV (MPV-2cREKR)

SupramoleculeName: Prefusion of HMPV (MPV-2cREKR) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human metapneumovirus

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Macromolecule #1: Prefusion of HMPV (MPV-2c)

MacromoleculeName: Prefusion of HMPV (MPV-2c) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus
Molecular weightTheoretical: 56.553586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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