+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11728 | |||||||||
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Title | SARS-CoV-2 spike glycoprotein bound to nanobodies (Ty1) | |||||||||
Map data | half map 2 | |||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||
Authors | Hallberg BM / Das H | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Authors: Leo Hanke / Laura Vidakovics Perez / Daniel J Sheward / Hrishikesh Das / Tim Schulte / Ainhoa Moliner-Morro / Martin Corcoran / Adnane Achour / Gunilla B Karlsson Hedestam / B Martin ...Authors: Leo Hanke / Laura Vidakovics Perez / Daniel J Sheward / Hrishikesh Das / Tim Schulte / Ainhoa Moliner-Morro / Martin Corcoran / Adnane Achour / Gunilla B Karlsson Hedestam / B Martin Hällberg / Ben Murrell / Gerald M McInerney / Abstract: SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive ...SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19. #1: Journal: BiorXiv / Year: 2020 Title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction Authors: Hanke L / Vidakovics Perez L / Sheward DJ / Das H / Schulte T / Moliner-Morro A / Corcoran M / Achour A / Karlsson Hedestam G / Hallberg BM / Murrell B / McInerney GM | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11728.map.gz | 282.9 MB | EMDB map data format | |
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Header (meta data) | emd-11728-v30.xml emd-11728.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11728_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_11728.png | 40.2 KB | ||
Masks | emd_11728_msk_1.map | 299.1 MB | Mask map | |
Others | emd_11728_half_map_1.map.gz emd_11728_half_map_2.map.gz | 277.9 MB 277.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11728 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11728 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11728.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | half map 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11728_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: locally sharpened map
File | emd_11728_half_map_1.map | ||||||||||||
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Annotation | locally sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_11728_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)
Entire | Name: SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1) |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1)
Supramolecule | Name: SARS-CoV-2 spike glycoprotein with bound nanobodies (Ty1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 470 KDa |
-Macromolecule #1: SARS-CoV-2 spike glycoprotein
Macromolecule | Name: SARS-CoV-2 spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: SARS-CoV-2 spike glycoprotein / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK |
-Macromolecule #2: Nanobody Ty1
Macromolecule | Name: Nanobody Ty1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAQVQLVETG GGLVQPGGSL RLSCAASGFT FSSVYMNWVR QAPGKGPEWV SRISPNSGNI GYTDSVKGRF TISRDNAKNT LYLQMNNLKP EDTALYYCAI GLNLSSSSVR GQGTQVTVSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: A 3-ul aliquot of the sample solution was applied 335to glow-discharged CryoMatrix holey grids with amorphous alloy film (Zhenjiang Lehua Technology) in 336a Vitrobot Mk IV (Thermo Fisher ...Details: A 3-ul aliquot of the sample solution was applied 335to glow-discharged CryoMatrix holey grids with amorphous alloy film (Zhenjiang Lehua Technology) in 336a Vitrobot Mk IV (Thermo Fisher Scientific) at 4 degrees and 100% humidity (blot 10 s, blot force 3).. |
Details | Spike trimer (0.7 mg/ml) and Ty1 (1.3 mg/ml) were mixed 334in a 1:8 molar ratio and incubated on ice for 5 minutes. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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