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- EMDB-9891: Cryo-EM structure of spike protein of feline infectious peritonit... -

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Basic information

Entry
Database: EMDB / ID: EMD-9891
TitleCryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4
Map dataFIPV-UU4 spike protein (sharpened)
Sample
  • Organelle or cellular component: Feline Infectious Peritonitis Virus Spike Protein
    • Protein or peptide: Feline Infectious Peritonitis Virus Spike Protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsCoV spike protein / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesFeline infectious peritonitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsHsu STD / Yang TJ
Funding support Taiwan, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2311-B-002-028-MY3 Taiwan
Ministry of Science and Technology (Taiwan)107-2628-M-001-005-MY3 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans.
Authors: Tzu-Jing Yang / Yen-Chen Chang / Tzu-Ping Ko / Piotr Draczkowski / Yu-Chun Chien / Yuan-Chih Chang / Kuen-Phon Wu / Kay-Hooi Khoo / Hui-Wen Chang / Shang-Te Danny Hsu /
Abstract: Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) ...Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) structure of the serotype I FIPV spike (S) protein, which is responsible for host recognition and viral entry. Mass spectrometry provided site-specific compositions of densely distributed high-mannose and complex-type Nglycans that account for 1/4 of the total molecular mass; most of the N-glycans could be visualized by cryo-EM. Specifically, the N-glycans that wedge between 2 galectin-like domains within the S1 subunit of FIPV S protein result in a unique propeller-like conformation, underscoring the importance of glycosylation in maintaining protein structures. The cleavage site within the S2 subunit responsible for activation also showed distinct structural features and glycosylation. These structural insights provide a blueprint for a better molecular understanding of the pathogenesis of FIP.
History
DepositionApr 22, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jx7
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9891.png

Downloads & links

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Map

FileDownload / File: emd_9891.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFIPV-UU4 spike protein (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 440 pix.
= 382.8 Å		0.87 Å/pix.
x 440 pix.
= 382.8 Å		0.87 Å/pix.
x 440 pix.
= 382.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-16.756969999999999 - 31.220509
Average (Standard dev.)-0.008156647 (±0.89499307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 382.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z382.800382.800382.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-16.75731.221-0.008

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Supplemental data

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Additional map: FIPV-UU4 spike protein (unsharpened)

Fileemd_9891_additional.map
AnnotationFIPV-UU4 spike protein (unsharpened)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: FIPV-UU4 spike protein (unsharpened)

Fileemd_9891_additional_1.map
AnnotationFIPV-UU4 spike protein (unsharpened)
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 1

Fileemd_9891_half_map_1.map
AnnotationHalf_map_1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_9891_half_map_2.map
AnnotationHalf_map_2
Projections & Slices
AxesZYX

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Sample components

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Entire : Feline Infectious Peritonitis Virus Spike Protein

EntireName: Feline Infectious Peritonitis Virus Spike Protein
Components
  • Organelle or cellular component: Feline Infectious Peritonitis Virus Spike Protein
    • Protein or peptide: Feline Infectious Peritonitis Virus Spike Protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Feline Infectious Peritonitis Virus Spike Protein

SupramoleculeName: Feline Infectious Peritonitis Virus Spike Protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Feline infectious peritonitis virus
Molecular weightTheoretical: 720 kDa/nm

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Macromolecule #1: Feline Infectious Peritonitis Virus Spike Protein

MacromoleculeName: Feline Infectious Peritonitis Virus Spike Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Feline infectious peritonitis virus
Molecular weightTheoretical: 163.829844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DAPHGVTLPH FNTSHNNSKF ELNFYNFLQT WDIPPNTETI LGGYLPYCDH EDNCGWYNFV YNNKVGPNAK YSYINTQNLN IPNVHGVYF DVREHNSDGV WDQIDRVGLL IAIHGTSHYS LLMVLQDGVE ASQPHVAVKI CHWNPGNIST YHQFDVNLGD G GQCVFNQR ...String:
DAPHGVTLPH FNTSHNNSKF ELNFYNFLQT WDIPPNTETI LGGYLPYCDH EDNCGWYNFV YNNKVGPNAK YSYINTQNLN IPNVHGVYF DVREHNSDGV WDQIDRVGLL IAIHGTSHYS LLMVLQDGVE ASQPHVAVKI CHWNPGNIST YHQFDVNLGD G GQCVFNQR FSLDTVLTAN DFYGFQWTDT YVDIYLGGTI TKVWVVNDWS VVEASISSHW NALNYGYYIQ FVNRTTYYAY NS TGGSNYT HLQLTECHTD YCAGYAKNVF VPIDGKIPEG FSFSNWFLLT DKSTLVQGRV LSSQPVFVQC LRPVPTWSNN TAV VHFKND VFCPNVTADV LRFNLNFSDT DVYTDSTTDD QLHFTFEDNT TASITCYSSA NVTDNQPASG SISHTPFVSN SYLC FANFS HSSVSRQFLG ILPPTVREFA FGRDGSIFVN GYKYFSLQPI KSVNFSISSV ENYGFWTIAY TNYTDVMVDV NGTVI TRLF YCDSPLNRIK CQQLKHELPD GFYSASMLVK KDLPKTFVTM PQFYNWMNVT LHVVLNDIEK KADIILAGAP ELASLA DIH FEIAQANGSV VNVTSVCVQA RQLALFYKYT SLQGLYTYSN LVQLQNYDCP FSPQQFNNYL QFETLCFDVS PAVAGCK WS LVHDVKWRTQ FATITVSYKD GAMITTMPKA QLGFQDISNI VKDECTDYNI YGFQGTGIIR STTSRLVAGL YYTSASGD L LGFKISTTGE IFTVVPCDLT AQAAVINDEI VGAITATNQT DLFEFVNHTW SRSARGSSPS TVNTYTMPQF YYITKWNNG TSSNCTSVIT YSSFAICNTG EIKYVNVTHV EIVDDSVGVI KPVSTGNITI PKNFTVAVQA EYVQIQVKPV AVDCAKYVCN GNRHCLNLL TQYTSACQTI ENSLNLGARL ESLMLNDMIT VSDRSLEFAT VDKFNTTALG GEKLGGLYFD GLSSLLPPRV G MRSAVEDL LFNKVVTSGL GTVDDDYKKC SAGTDVADLV CAQYYNGIMV LPGVVDYNKM AMYTASLIGG MALGSITSAV AV PFSMQVQ ARLNYVALQT DVLQENQKIL ANAFNNAIGN ITLALGKVSN AITTVSDGFN SMASALTKIQ SVVNQQGEAL SHL ISQLQK NFQAISSSIA EIYNRLEKVE ADAQVDRLIT GRLAALNAYV AQTLTQYAEV KASRQLAMEK VNECVKSQSD RYGF CGNGT HLFSLVNSAP DGLLFFHTVL LPTEWEEVTA WSGICVNDTY AYLLKDFDHS IFSYNGTYMV TPRNMFQPRK PQMSD FVQI TSCEVTFLNT THTTFQEIVI DYIDINKTIA DMLEQYHSNY TTPELDLQLE IFNQTKLNLT AEIDQLEQRA DNLTNI AHE LQQYIDNLNK TIVDLEWLNR IETYVKWPGS GGYIPEAPRD GQAYVRKDGE WVLLSTFLKG QDNSADIQHS GGRSSLE GP RFEGKPIPNP LLGLDSTRTG HHHHHH

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #10: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 10 / Number of copies: 6 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 1X D-PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blot for 3 seconds before plunging; blot force: 0; waiting time: 10s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2436 / Average exposure time: 2.5 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 442004
Startup modelType of model: INSILICO MODEL / Details: Generated by cisTEM
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 102586
Initial angle assignmentType: RANDOM ASSIGNMENT / Software: (Name: cisTEM, RELION)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software: (Name: cisTEM, RELION)

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