+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37632 | |||||||||
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Title | Cryo-EM structure of bat RsSHC014 spike glycoprotein | |||||||||
Map data | ||||||||||
Sample |
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Keywords | spike / 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 | Bat SARS-like coronavirus RsSHC014 / Enterobacteria phage T6 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Wang X / Qiao S | |||||||||
Funding support | 1 items
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Citation | Journal: J.Virol. / Year: 2024 Title: Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1 Authors: Qiao S / Wang X | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37632.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-37632-v30.xml emd-37632.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_37632.png | 51.9 KB | ||
Filedesc metadata | emd-37632.cif.gz | 6.1 KB | ||
Others | emd_37632_half_map_1.map.gz emd_37632_half_map_2.map.gz | 77.5 MB 77.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37632 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37632 | HTTPS FTP |
-Validation report
Summary document | emd_37632_validation.pdf.gz | 697.2 KB | Display | EMDB validaton report |
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Full document | emd_37632_full_validation.pdf.gz | 696.8 KB | Display | |
Data in XML | emd_37632_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_37632_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37632 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37632 | HTTPS FTP |
-Related structure data
Related structure data | 8wluMC 8wlyC 8wlzC 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_37632.map.gz / Format: CCP4 / Size: 98.9 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: 1.0979 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_37632_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37632_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RsSHC014 glycoprotein
Entire | Name: RsSHC014 glycoprotein |
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Components |
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-Supramolecule #1: RsSHC014 glycoprotein
Supramolecule | Name: RsSHC014 glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bat SARS-like coronavirus RsSHC014 |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacteria phage T6 (virus) |
Molecular weight | Theoretical: 140.530312 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFRDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD ...String: MKLLVLVFAT LVSSYTIEKC LDFDDRTPPA NTQFLSSHRG VYYPDDIFRS NVLHLVQDHF LPFDSNVTRF ITFGLNFDNP IIPFRDGIY FAATEKSNVI RGWVFGSTMN NKSQSVIIMN NSTNLVIRAC NFELCDNPFF VVLKSNNTQI PSYIFNNAFN C TFEYVSKD FNLDLGEKPG NFKDLREFVF RNKDGFLHVY SGYQPISAAS GLPTGFNALK PIFKLPLGIN ITNFRTLLTA FP PRPDYWG TSAAAYFVGY LKPTTFMLKY DENGTITDAV DCSQNPLAEL KCSVKSFEID KGIYQTSNFR VAPSKEVVRF PNI TNLCPF GEVFNATTFP SVYAWERKRI SNCVADYSVL YNSTSFSTFK CYGVSATKLN DLCFSNVYAD SFVVKGDDVR QIAP GQTGV IADYNYKLPD DFLGCVLAWN TNSKDSSTSG NYNYLYRWVR RSKLNPYERD LSNDIYSPGG QSCSAVGPNC YNPLR PYGF FTTAGVGHQP YRVVVLSFEL LNAPATVCGP KLSTDLIKNQ CVNFNFNGLT GTGVLTPSSK RFQPFQQFGR DVSDFT DSV RDPKTSEILD ISPCSFGGVS VITPGTNTSS EVAVLYQDVN CTDVPVAIHA DQLTPSWRVY STGNNVFQTQ AGCLIGA EH VDTSYECDIP IGAGICASYH TVSSLRSTSQ KSIVAYTMSL GADSSIAYSN NTIAIPTNFS ISITTEVMPV SMAKTSVD C NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAVEQDRNT REVFAQVKQM YKTPTLKDFG GFNFSQILPD PLKPTKRSF IEDLLFNKVT LADAGFMKQY GECLGDINAR DLICAQKFNG LTVLPPLLTD DMIAAYTAAL VSGTATAGWT FGAGAALQIP FAMQMAYRF NGIGVTQNVL YENQKQIANQ FNKAISQIQE SLTTTSTALG KLQDVVNQNA QALNTLVKQL SSNFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQA AP HGVVFLH VTYVPSQERN FTTAPAICHE GKAYFPREGV FVFNGTSWFI TQRNFFSPQI ITTDNTFVSG SCDVVIGIIN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAP RDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKGGGSG GGGSGGSAWS HPQFEK UniProtKB: Spike glycoprotein, Fibritin |
-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: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 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: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 250439 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |