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- EMDB-41825: Prefusion-stabilized Langya virus F protein, variant G99C/I109C -

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Basic information

Entry
Database: EMDB / ID: EMD-41825
TitlePrefusion-stabilized Langya virus F protein, variant G99C/I109C
Map data
Sample
  • Complex: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
    • Protein or peptide: Fusion glycoprotein F
KeywordsLangya / Langya virus / LayV / fusion / F / LayV F / VIRAL PROTEIN / disulfide / prefusion / prefusion-stabilized / vaccine design / VIRUS
Biological speciesLangya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsByrne PO / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
Authors: Byrne PO / Blade EG / McLellan JS
History
DepositionSep 1, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41825.png

Downloads & links

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Map

FileDownload / File: emd_41825.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.94 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.81844723 - 1.414063
Average (Standard dev.)-0.00051162386 (±0.03859037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 240.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41825_msk_1.map
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AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_41825_additional_1.map
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Half map: #2

Fileemd_41825_half_map_1.map
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Histogram

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Half map: #1

Fileemd_41825_half_map_2.map
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Sample components

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Entire : Prefusion-stabilized Langya virus F protein, variant G99C/I109C

EntireName: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
Components
  • Complex: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
    • Protein or peptide: Fusion glycoprotein F

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Supramolecule #1: Prefusion-stabilized Langya virus F protein, variant G99C/I109C

SupramoleculeName: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus

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Macromolecule #1: Fusion glycoprotein F

MacromoleculeName: Fusion glycoprotein F / type: protein_or_peptide / ID: 1
Details: Prefusion-stabilized Langya virus F protein, variant G99C/I109C
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 60.590789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSC NNKYRFAGAC MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID ...String:
MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSC NNKYRFAGAC MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID TIRGEINNNI IPVINQLSCD TIGLSVGIKL TQYYSEILTA FGPALQNPVN TRITIQAISS VFNRNFDELL KI MGYTSGD LYEILHSGLI RGNIIDVDVE AGYIALEIEF PNLTLVPNAV VQELMPISYN VDGDEWVTLV PRFVLTRTTL LSN IDTSRC TVTESSVICD NDYALPMSYE LIGCLQGDTS KCAREKVVSS YVPRFALSDG LVYANCLNTI CRCMDTDTPI SQSL GTTVS LLDNKKCLVY QVGDILISVG SYLGEGEYSA DNVELGPPVV IDKIDIGNQL AGINQTLQNA EDYIEKSEEG GSGYI PEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWSHPQFE K

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.0 e/Å2

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Image processing

Particle selectionNumber selected: 321161
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 72726
FSC plot (resolution estimation)

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