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- EMDB-34422: Structure of SARS-CoV-1 Spike Protein with Engineered x2 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 x2 Disulfide (G400C and V969C), Locked-2 Conformation | |||||||||
![]() | 9-29 | |||||||||
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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: 3.44681 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 | ![]() | 32.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 107.8 KB | ||
Masks | ![]() | 52.7 MB | ![]() | |
Others | ![]() ![]() | 40.9 MB 41 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h12MC ![]() 8h0xC ![]() 8h0yC ![]() 8h0zC ![]() 8h10C ![]() 8h11C ![]() 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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Annotation | 9-29 | ||||||||||||||||||||
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
-Mask #1
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Density Histograms |
-Half map: 9-29
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Density Histograms |
-Half map: 9-29
File | emd_34422_half_map_2.map | ||||||||||||
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Annotation | 9-29 | ||||||||||||
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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: 130.916188 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DLDRCTTFDD VQAPNYTQHT SSMRGVYYPD EIFRSDTLYL TQDLFLPFYS NVTGFHTINH TFGNPVIPFK DGIYFAATEK SNVVRGWVF GSTMNNKSQS VIIINNSTNV VIRACNFELC DNPFFAVSKP MGTQTHTMIF DNAFNCTFEY ISDAFSLDVS E KSGNFKHL ...String: DLDRCTTFDD VQAPNYTQHT SSMRGVYYPD EIFRSDTLYL TQDLFLPFYS NVTGFHTINH TFGNPVIPFK DGIYFAATEK SNVVRGWVF GSTMNNKSQS VIIINNSTNV VIRACNFELC DNPFFAVSKP MGTQTHTMIF DNAFNCTFEY ISDAFSLDVS E KSGNFKHL REFVFKNKDG FLYVYKGYQP IDVVRDLPSG FNTLKPIFKL PLGINITNFR AILTAFSPAQ DIWGTSAAAY FV GYLKPTT FMLKYDENGT ITDAVDCSQN PLAELKCSVK SFEIDKGIYQ TSNFRVVPSG DVVRFPNITN LCPFGEVFNA TKF PSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPC QTGVIADYNY KLPD DFMGC VLAWNTRNID ATSTGNYNYK YRYLRHGKLR PFERDISNVP FSPDGKPCTP PALNCYWPLN DYGFYTTTGI GYQPY RVVV LSFELLNAPA TVCGPKLSTD LIKNQCVNFN FNGLTGTGVL TPSSKRFQPF QQFGRDVSDF TDSVRDPKTS EILDIS PCS FGGVSVITPG TNASSEVAVL YQDVNCTDVS TAIHADQLTP AWRIYSTGNN VFQTQAGCLI GAEHVDTSYE CDIPIGA GI CASYHTVSLL RSTSQKSIVA YTMSLGADSS IAYSNNTIAI PTNFSISITT EVMPVSMAKT SVDCNMYICG DSTECANL L LQYGSFCTQL NRALSGIAAE QDRNTREVFA QVKQMYKTPT LKYFGGFNFS QILPDPLKPT KRSFIEDLLF NKVTLADAG FMKQYGECLG DINARDLICA QKFNGLTVLP PLLTDDMIAA YTAALVSGTA TAGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQK QIANQFNKAI SQIQESLTTT STALGKLQDV VNQNAQALNT LVKQLSSNFG AISSVLNDIL SRLDKCEAEV Q IDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQAAPHGV VFLHVTYVPS QE RNFTTAP AICHEGKAYF PREGVFVFNG TSWFITQRNF FSPQIITTDN TFVSGNCDVV IGIINNTVYD PLQPELDSFK EEL DKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIK 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: 39 / 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 | 6.5 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 TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.6 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |