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- EMDB-41150: Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 00... -

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Basic information

Entry
Database: EMDB / ID: EMD-41150
TitleCryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 007 in Closed Conformation
Map data
Sample
  • Virus: Civet SARS CoV 007/2004 (virus)
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water
KeywordsSpike / Glycoprotein / Coronavirus / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesPaguma larvata (masked palm civet) / Civet SARS CoV 007/2004 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsBostina M / Hills FR / Eruera AR
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Other private New Zealand
CitationJournal: To Be Published
Title: Cryo-EM reveals variationo in structural motifs within animal SARS-related coronavirus spike protein
Authors: Bostina M / Hills FR / Eruera AR
History
DepositionJun 29, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41150.png

Downloads & links

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Map

FileDownload / File: emd_41150.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.0445
Minimum - Maximum-0.43404052 - 0.99841297
Average (Standard dev.)-0.00024364273 (±0.024573533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41150_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_41150_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 : Civet SARS CoV 007/2004

EntireName: Civet SARS CoV 007/2004 (virus)
Components
  • Virus: Civet SARS CoV 007/2004 (virus)
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water

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Supramolecule #1: Civet SARS CoV 007/2004

SupramoleculeName: Civet SARS CoV 007/2004 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 285945 / Sci species name: Civet SARS CoV 007/2004 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Paguma larvata (masked palm civet)
Molecular weightTheoretical: 122.479953 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: LDRCTTFDDV QAPNYTQHTS SMRGVYYPDE IFRSDTLYLT QDLFLPFYSN VTGFHTINHT FDNPVIPFKD GIYFAATEKS NVVRGWVFG STMNNKSQSV IIINNSTNVV IRACNFELCD NPFFVVSKPM GTQTHTMIFD NAFNCTFEYI SDAFSLDVSE K SGNFKHLR ...String:
LDRCTTFDDV QAPNYTQHTS SMRGVYYPDE IFRSDTLYLT QDLFLPFYSN VTGFHTINHT FDNPVIPFKD GIYFAATEKS NVVRGWVFG STMNNKSQSV IIINNSTNVV IRACNFELCD NPFFVVSKPM GTQTHTMIFD NAFNCTFEYI SDAFSLDVSE K SGNFKHLR EFVFKNKDGF LYVYKGYQPI DVVRDLPSGF NTLKPIFKLP LGIKITNFRA ILTAFSPAQG TWGTSAAAYF VG YLKPTTF MLKYDENGTI TDAVDCSQNP LAELKCSVKS FEIDKGIYQT SNFRVVPSGD VVRFPNITNL CPFGEVFNAT KFP SVYAWE RKRISNCVAD YSVLYNSTSF STFKCYGVSA TKLNDLCFSN VYADSFVVKG DDVRQIAPGQ TGVIADYNYK LPDD FMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SSDGKPCTPP APNCYWPLRG YGFYTTSGIG YQPYR VVVL SFELLNAPAT VCGPKLSTDL IKNQCVNFNF NGLTGTGVLT PSSKRFQPFQ QFGRDVSDFT DSVRDPKTSE ILDISP CSF GGVSVITPGT NASSEVAVLY QDVNCTDVST LIHAEQLTPA WRIYSTGNNV FQTQAGCLIG AEHVDTSYEC DIPIGAG IC ASYHTVSSLR STSQKSIVAY TMSLGADSSI AYSNNTIAIP TNFSISITTE VMPVSMAKTS VDCNMYICGD STECANLL L QYGSFCRQLN RALSGIAAEQ DRNTREVFVQ VKQMYKTPTL KDFGGFNFSQ ILPDPLKPTK RSFIEDLLFN KVTLADAGF MKQYGECLGD INARDLICAQ KFNGLTVLPP LLTDDMIAAY TAALVSGTAT AGWTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKQ IANQFNKAIS QIQESLTTTS TALGKLQDVV NQNAQALNTL VKQLSSNFGA ISSVLNDILS RLDKVEAEVQ I DRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQAAPHGVV FLHVTYVPSQ ER NFTTAPA ICHEGKAYFP REGVFVFSGT SWFITQRNFF SPQIITTDNT FVSGNCDVVI GIINNTVYD

UniProtKB: Spike glycoprotein

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

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #5: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID / Linoleic acid

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 582 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7e7b

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 800000

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