+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32492 | |||||||||
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Title | SARS-CoV-2 spike glycoprotein trimer in Intermediate state | |||||||||
Map data | SARS-CoV-2 spike protein after treatment with Cathepsin L | |||||||||
Sample |
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Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Zhu Y / Tai L / Yin G / Sun F | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Discov / Year: 2022 Title: Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies Authors: Zhao MM / Zhu Y / Zhang L / Zhong G / Tai L / Liu S / Yin G / Lu J / He Q / Li MJ / Zhao RX / Wang H / Huang W / Fan C / Shuai L / Wen Z / Wang C / He X / Chen Q / Liu B / Xiong X / Bu Z / ...Authors: Zhao MM / Zhu Y / Zhang L / Zhong G / Tai L / Liu S / Yin G / Lu J / He Q / Li MJ / Zhao RX / Wang H / Huang W / Fan C / Shuai L / Wen Z / Wang C / He X / Chen Q / Liu B / Xiong X / Bu Z / Wang Y / Sun F / Yang JK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32492.map.gz | 59.1 MB | EMDB map data format | |
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Header (meta data) | emd-32492-v30.xml emd-32492.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32492_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_32492.png | 17.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32492 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32492 | HTTPS FTP |
-Validation report
Summary document | emd_32492_validation.pdf.gz | 489.4 KB | Display | EMDB validaton report |
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Full document | emd_32492_full_validation.pdf.gz | 489 KB | Display | |
Data in XML | emd_32492_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_32492_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32492 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32492 | HTTPS FTP |
-Related structure data
Related structure data | 7wgyMC 7wgvC 7wgxC 7wgzC 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_32492.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 spike protein after treatment with Cathepsin L | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer
Entire | Name: SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer |
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Components |
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-Supramolecule #1: SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer
Supramolecule | Name: SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-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: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 133.656984 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GD SSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NIT NLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPG QTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQ SYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQQFGR DIADTT DAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQDVN CTEVPVAIHA DQLTPTWRVY STGSNVFQTR AGCLIGA EH VNNSYECDIP IGAGICASYQ TQTNSRSVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVD C TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKDFG GFNFSQILPD PSKPSKRSF IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGAALQIP FAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTASALG KLQDVVNQNA QALNTLVKQL SSNFGAISSV L NDILSRLD KVEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS AP HGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQYIKGS GREN LYFQ |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 15 / 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 | 2 mg/mL |
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Buffer | pH: 5.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 80.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |