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- EMDB-64076: The structure of FIPV spike glycoprotein -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64076
TitleThe structure of FIPV spike glycoprotein
Map data
Sample
  • Complex: FIPV spike glycoprotein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsprotein / PROTEIN BINDING
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 / Fibritin C-terminal / Fibritin C-terminal region / 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 superfamily, coronavirus ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Fibritin C-terminal / Fibritin C-terminal region / 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 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesFeline coronavirus (strain FIPV WSU-79/1146) / Enterobacteria phage T6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsSun JQ / Niu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: To Be Published
Title: The structure of FIPV spike glycoprotein
Authors: Sun JQ
History
DepositionApr 8, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64076.png

Downloads & links

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Map

FileDownload / File: emd_64076.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.182
Minimum - Maximum-0.51546574 - 1.1229681
Average (Standard dev.)-0.00068353466 (±0.033025853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64076_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64076_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 : FIPV spike glycoprotein

EntireName: FIPV spike glycoprotein
Components
  • Complex: FIPV spike glycoprotein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: FIPV spike glycoprotein

SupramoleculeName: FIPV spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Feline coronavirus (strain FIPV WSU-79/1146)

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T6 (virus)
Molecular weightTheoretical: 159.548406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTNNECIQVN VTQLAGNENL IRDFLFSNFK EEGSNVVGGY YPTEVWYNCS RTARTTAFQY FNNIHAFYFV MEAMENSTGN ARGKPLLFH VHGEPVSVII SAYRDDVQQR PLLKHGLVCI TKNRHINYEQ FTSNQWNSTC TGADRKIPFS VIPTDNGTKI Y GLEWNDDF ...String:
TTNNECIQVN VTQLAGNENL IRDFLFSNFK EEGSNVVGGY YPTEVWYNCS RTARTTAFQY FNNIHAFYFV MEAMENSTGN ARGKPLLFH VHGEPVSVII SAYRDDVQQR PLLKHGLVCI TKNRHINYEQ FTSNQWNSTC TGADRKIPFS VIPTDNGTKI Y GLEWNDDF VTAYISGRSY HLNINTNWFN NVTLLYSRSS TATWEYSAAY AYQGVSNFTY YKLNNTNGLK TYELCEDYEH CT GYATNVF APTSGGYIPD GFSFNNWFLL TNSSTFVSGR FVTNQPLLIN CLWPVPSFGV AAQEFCFEGA QFSQCNGVSL NNT VDVIRF NLNFTADVQS GMGATVFSLN TTGGVILEIS CYSDTVSESS SYSYGEIPFG ITDGPIYCYV LYNGTALKYL GTLP PSVKE IAISKWGHFY INGYNFFSTF PIGCISFNLT TGVSGAFWTI AYTSYTEALV QVENTAIKNV TYCNSHINNI KCSQL TANL NNGFYPVASS EVGFVNKSVV LLPSFFTYTA VNITIDLGMK LSGYGQPIAS TLSNITLPMQ DNNTDVYCIR SNQFSV YVH STCKSSLWDN IFNQDCTDVL EATAVIKTGT CPFSFDKLNN YLTFNKFCLS LSPVGANCKF DVAARTRTNE QVVRSLY VI YEEGDNIVGV PSDNSGLHDL SVLHLDSCTD YNIYGRTGVG IIRRTNSTLL SGLYYTSLSG DLLGFKNVSD GVIYSVTP C DVSVQAAVID GAIVGAMTSI NSELLGLTHW TTTPNFYYYS IYNYTSERTR GTAIDSNDVD CEPVITYSNI GVCKNGALV FINVTHSDGD VQPISTGNVT IPTNFTISVQ VEYMQVYTTP VSIDCARYVC NGNPRCNKLL TQYVSACQTI EQALAMGARL ENMEVDSML FVSENALKLA SVEAFNSTEN LDPIYKEWPS IGGSWLGGLK DILPSHNSKR KYGSAIEDLL FDKVVTSGLG T VDEDYKRC TGGYDIADLV CAQYYNGIMV LPGVANADKM TMYTASLAGG ITLGALGGGA VAIPFAVAVQ ARLNYVALQT DV LNKNQQI LANAFNQAIG NITQAFGKVN DAIHQTSQGL ATVAKALAKV QDVVNTQGQA LSHLTVQLQN NFQAISSSIS DIY NRLDPP SADAQVDRLI TGRLTALNAF VSQTLTRQAE VRASRQLAKD KVNECVRSQS QRFGFCGNGT HLFSLANAAP NGMI FFHTV LLPTAYETVT AWSGICASDG DRTFGLVVKD VQLTLFRNLD DKFYLTPRTM YQPRVATSSD FVQIEGCDVL FVNAT VIDL PSIIPDYIDI NQTVQDILEN YEPNWTVPEF TLDIFNATYL NLTGEIDDLE FRSEKLHNTT VELAILIDNI NNTLVN LEW LNRIETYVKG GGSGGGSGYI PEAPRDGQAY VRKDGEWVLL STFLGSGGGS AWSHPQFEKG GGSGGGSGGS SAWSHPQ FE KHHHHHHHH

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / 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: 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83781
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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