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Yorodumi- EMDB-41150: Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 00... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41150 | |||||||||
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Title | Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 007 in Closed Conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Spike / 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 | |||||||||
Biological species | Civet SARS CoV 007/2004 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.92 Å | |||||||||
Authors | Bostina M / Hills FR / Eruera AR | |||||||||
Funding support | New Zealand, 1 items
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Citation | Journal: PLoS Pathog / Year: 2024 Title: Variation in structural motifs within SARS-related coronavirus spike proteins. Authors: Francesca R Hills / Alice-Roza Eruera / James Hodgkinson-Bean / Fátima Jorge / Richard Easingwood / Simon H J Brown / James C Bouwer / Yi-Ping Li / Laura N Burga / Mihnea Bostina / Abstract: SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species ...SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41150.map.gz | 123 MB | EMDB map data format | |
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Header (meta data) | emd-41150-v30.xml emd-41150.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_41150.png | 66.5 KB | ||
Filedesc metadata | emd-41150.cif.gz | 6.3 KB | ||
Others | emd_41150_half_map_1.map.gz emd_41150_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41150 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41150 | HTTPS FTP |
-Validation report
Summary document | emd_41150_validation.pdf.gz | 805.5 KB | Display | EMDB validaton report |
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Full document | emd_41150_full_validation.pdf.gz | 805 KB | Display | |
Data in XML | emd_41150_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_41150_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41150 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41150 | HTTPS FTP |
-Related structure data
Related structure data | 8tc1MC 8tc0C 8tc5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41150.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41150_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41150_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Civet SARS CoV 007/2004
Entire | Name: Civet SARS CoV 007/2004 (virus) |
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Components |
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-Supramolecule #1: Civet SARS CoV 007/2004
Supramolecule | Name: 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
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Civet SARS CoV 007/2004 (virus) |
Molecular weight | Theoretical: 122.479953 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 15 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #5: LINOLEIC ACID
Macromolecule | Name: LINOLEIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: EIC |
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Molecular weight | Theoretical: 280.445 Da |
Chemical component information | ChemComp-EIC: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 582 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 800000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |