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- EMDB-34421: Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfid... -
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Open data
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Basic information
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Title | Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Closed Conformation | |||||||||
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![]() | PROTEIN ENGINEERING / SPIKE PROTEIN / SARS-COV-1 / SARS-COV / VIRAL PROTEIN | |||||||||
Function / homology | ![]() Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
![]() | Zhang X / Li Z / Liu Y / Wang J / Fu L / Wang P / He J / Xiong X | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun ...Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun He / Jincun Zhao / Xiaoli Xiong / ![]() Abstract: SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers ...SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 85.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 108.9 KB | ||
Masks | ![]() | 144.7 MB | ![]() | |
Others | ![]() ![]() | 114.2 MB 114.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h11MC ![]() 8h0xC ![]() 8h0yC ![]() 8h0zC ![]() 8h10C ![]() 8h12C ![]() 8h13C ![]() 8h14C ![]() 8h15C ![]() 8h16C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.095 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : SARS-CoV-1 spike protein
Entire | Name: SARS-CoV-1 spike protein |
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Components |
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-Supramolecule #1: SARS-CoV-1 spike protein
Supramolecule | Name: SARS-CoV-1 spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 410 KDa |
-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: ![]() |
Molecular weight | Theoretical: 136.679359 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ETGTDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC TFEYISDAFS L DVSEKSGN ...String: ETGTDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC TFEYISDAFS L DVSEKSGN FKHLREFVFK NKDGFLYVYK GYQPIDVVRD LPSGFNTLKP IFKLPLGINI TNFRAILTAF SPAQDIWGTS AA AYFVGYL KPTTFMLKYD ENGTITDAVD CSQNPLAELK CSVKSFEIDK GIYQTSNFRV VPSGDVVRFP NITNLCPFGE VFN ATKFPS VYAWERKKIS NCVADYSVLY NSTFFSTFKC YGVCATKLND LCFSNVYADS FVVKGDDVRQ IAPGQTGVIA DYNY KLPDD FMGCVLAWNT RNIDATSTGN YNYKYRYLRH GKLRPFERDI SNVPFSPDGK PCTPPALNCY WPLNDYGFYT TTGIG YQPY RVVVLSFELL NAPATVCGPK LSTDLIKNQC VNFNFNGLTG TGVLTPSSKR FQPFQQFGRD VSDFTDSVRD PKTSEI LDI SPCSFGGVSV ITPGTNASSE VAVLYQDVNC TDVSTAIHAD QLTPAWRIYS TGNNVFQTQA GCLIGAEHVD TSYECDI PI GAGICASYHT VSLLRSTSQK SIVAYTMSLG ADSSIAYSNN TIAIPTNFSI SITTEVMPVS MAKTSVDCNM YICGDSTE C ANLLLQYGSF CTQLNRALSG IAAEQDRNTR EVFAQVKQMY KTPTLKYFGG FNFSQILPDP LKPTKRSFIE DLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLY ENQKQIANQF NKAISQIQES LTTTSTALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLCKV E AEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PHGVVFLHVT YV PSQERNF TTAPAICHEG KAYFPREGVF VFNGTSWFIT QRNFFSPQII TTDNTFVSGN CDVVIGIINN TVYDPLQPEL DSF KEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQYIKGSG RENLYFQGGG GSGY IPEAP RDGQAYVRKD GEWVLLSTFL GHHHHHH UniProtKB: Spike glycoprotein |
-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: 37 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.7 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
Details: Gibco PBS C10010 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.37 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |