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- EMDB-46716: Molecular basis of pathogenicity of the recently emerged FCoV-23 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-46716
TitleMolecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus. FCoV-23 S long domain 0 in swung-out conformation (local refinement)
Map dataMain map
Sample
  • Complex: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
    • Protein or peptide: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsCoronavirus / alphacoronavirus / feline coronavirus / cryo-EM / neutralization assays / binding assays / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Biological speciesFeline coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsTortorici MA / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Nature / Year: 2025
Title: Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics
Authors: Tortorci MA / Choi A / Gibson CA / Lee J / Brown JT / Stewart C / Joshi A / Harari S / Willoughby I / Treichel C / Leaf EM / Bloom JD / King NP / Tait-Burkard C / Whittaker GR / Veesler D
History
DepositionAug 23, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46716.png

Downloads & links

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Map

FileDownload / File: emd_46716.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 512 pix.
= 515.891 Å		1.01 Å/pix.
x 512 pix.
= 515.891 Å		1.01 Å/pix.
x 512 pix.
= 515.891 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.37
Minimum - Maximum-4.595756 - 6.478615
Average (Standard dev.)-0.00015952557 (±0.059652176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 515.8912 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_46716_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_46716_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_46716_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FCoV-23 S long domain 0 in swung-out conformation (local refinement)

EntireName: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
Components
  • Complex: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
    • Protein or peptide: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: FCoV-23 S long domain 0 in swung-out conformation (local refinement)

SupramoleculeName: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Feline coronavirus

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Macromolecule #1: FCoV-23 S long domain 0 in swung-out conformation (local refinement)

MacromoleculeName: FCoV-23 S long domain 0 in swung-out conformation (local refinement)
type: protein_or_peptide / ID: 1 / Details: S long domain 0 in swung-out conformation / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Feline coronavirus / Strain: FCoV-23
Molecular weightTheoretical: 162.599625 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTIKPNNDCR QVNVTQLDGN ENLIRDFLFQ NFKEEGTVVV GGYYPTEVWY NCSKTLTTT AYAYFNNIHA FYFDMEAMEN STGNARGKPL LFHVHGEPVS VIIYISAYGD DVQHRPLLKH GLVCITKTRN V DYNSFTSS ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTIKPNNDCR QVNVTQLDGN ENLIRDFLFQ NFKEEGTVVV GGYYPTEVWY NCSKTLTTT AYAYFNNIHA FYFDMEAMEN STGNARGKPL LFHVHGEPVS VIIYISAYGD DVQHRPLLKH GLVCITKTRN V DYNSFTSS QWNSICTGND RKVPFSVIPT DNGTKIYGLE WNDELVTAYI SGRSYNWNIN NNWFNNVTLM YSRSSTATWL HS AAYVYQG VSNFTYYKLN NTNGLKTYEF CEDYEYCTGY ATNVFAPTVG GYIPDGFSFN NWFLLTNDST FVSGRFVTNQ PLL VNCLWP VPSFGVAAQE FCFEGAQFSQ CNGVSLNNTV DVIRFNLNFT ADVQSGMGAT VFSLNTTGGV ILEISCYNDT VRES SFYSY GEIPFGITDG PKYCYVLYNG TALKYLGTLP PSVKEIAISK WGHFYINGYN FFSTFPIDCI SFNLTTSTSG AFWTI AYTS YTEALVQVEN TAIKKVTYCN SHINNIKCSQ LTANLQNGFY PVASSEVGLV NKSVVLLPSF YSHTSVNITI DLGMKL SGY GQPIASALSN ITLPMQDNNT DVYCIRSNQF SVYVHSTCKS SLWDNVFNSD CTDVLHATAV IKTGTCPFSF DKLNNYL TF NKFCLSLHPV GANCKFDVAA RTRTNEQVVR SLYVIYEEGD NIAGVPSDNS GLHDLSVLHL DSCTDYNIYG KTGIGIIR Q TNSTLLSGLY YTSLSGDLLG FKNVTDGVVY SVTPCDVSAQ AAVIDGTIVG AMTSINSELL GLTHWTTTPN FYYYSIYNY TNERTRGTAI DSNDVDCEPI ITYSNIGVCK NGALVFINVT HSDGDVQPIS TGNVTIPTNF TISVQVEYIQ VYTTPVSIDC SRYVCNGNP RCNKLLTQYV SACQTIEQAL AMGARLENME VDSMLFVSEN ALKLASVEAF NSTEHLDPIY KEWPNIGGSW L GGLKDILP SHNSKRKYRS AIEDLLFDKV VTSGLGTVDE DYKRCTGGYD IADLVCAQYY NGIMVLPGVA NDDKMTMYTA SL AGGITLG ALGGGAVAIP FAVAVQARLN YVALQTDVLN KNQQILANAF NQAIGNITQA FGKVNDAIHQ TSKGLATVAK ALA KVQDVV NTQGQALSHL TVQLQNNFQA ISSSISDIYN RLDPPSADAQ VDRLITGRLT ALNAFVSQTL TRQAEVRASR QLAK DKVNE CVRSQSQRFG FCGNGTHLFS LANAAPNGMI FFHTVLLPTA YETVTAWSGI CASDGDHTFG LVVKDVQLTL FRNLD DKFY LTPRTMYQPR VATISDFVQI EGCDVLFVNA TVIELPGIIP DYIDINQTVQ DILENYRPNW TVPELTLDIF NSTYLN LTG EINDLEFRSE KLHNTTVELA VLIDNINNTL VNLEWLNRIE TYVKSGGYIP EAPRDGQAYV RKDGEWVLLS TFLVPRG SG GSGGSGLNDI FEAQKIEWHE GGSHHHHHHH H

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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: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 28 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 539331
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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