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Yorodumi- EMDB-24257: Potent neutralizing nanobodies resist convergent circulating vari... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24257 | ||||||||||||
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Title | Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB34 | ||||||||||||
Map data | CryoEM map of CovS with NB34 | ||||||||||||
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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / Lama glama (llama) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||
Authors | Sun D / Zhang C / Shi Y | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: bioRxiv / Year: 2021 Title: Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes. Authors: Dapeng Sun / Zhe Sang / Yong Joon Kim / Yufei Xiang / Tomer Cohen / Anna K Belford / Alexis Huet / James F Conway / Ji Sun / Derek J Taylor / Dina Schneidman-Duhovny / Cheng Zhang / Wei Huang / Yi Shi / Abstract: There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel ...There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics. | ||||||||||||
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_24257.map.gz | 254.9 MB | EMDB map data format | |
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Header (meta data) | emd-24257-v30.xml emd-24257.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_24257.png | 69.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24257 | HTTPS FTP |
-Validation report
Summary document | emd_24257_validation.pdf.gz | 578 KB | Display | EMDB validaton report |
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Full document | emd_24257_full_validation.pdf.gz | 577.5 KB | Display | |
Data in XML | emd_24257_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_24257_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24257 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24257 | HTTPS FTP |
-Related structure data
Related structure data | 7n9eMC 7n9aC 7n9bC 7n9cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24257.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of CovS with NB34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS Cov 2 Spike S with Nanobody Nb34
Entire | Name: SARS Cov 2 Spike S with Nanobody Nb34 |
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Components |
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-Supramolecule #1: SARS Cov 2 Spike S with Nanobody Nb34
Supramolecule | Name: SARS Cov 2 Spike S with Nanobody Nb34 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: SARS Cov 2 Spike S
Supramolecule | Name: SARS Cov 2 Spike S / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) Recombinant plasmid: Mammalian expression vector BsrGI-MCS-pcDNA3.1 |
-Supramolecule #3: Nanobody Nb34
Supramolecule | Name: Nanobody Nb34 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Lama glama (llama) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
-Macromolecule #1: Nb34 nanobody
Macromolecule | Name: Nb34 nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 16.951646 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASMTGGQQM GRDPNSDVQL VESGGGLVQA GGSLRLSCAA SGFTFSNYVM YWGRQAPGKG REWVSGIDSD GSDTAYASSV KGRFTISRD NAKNTLYLQM NNLKPEDTAL YYCVKSKDPY GSPWTRSEFD DYWGQGTQVT VSSKLAAALE HHHHHH |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 Details: Pre-fusion stabilized HexaPro construct, including six proline substitutions and furin cleavage site RRAR 682-685 mutated to GSAS Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 152.31275 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFG TATMFVFLVL LPLVSSQCVN LTTRTQLPPA YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA I HVSGTNGT ...String: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFG TATMFVFLVL LPLVSSQCVN LTTRTQLPPA YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA I HVSGTNGT KRFDNPVLPF NDGVYFASTE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLGVYYH KN NKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPINLVRD LPQGFSALEP LVD LPIGIN ITRFQTLLAL HRSYLTPGDS SSGWTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTV EKGIY QTSNFRVQPT ESIVRFPNIT NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLN DLCF TNVYADSFVI RGDEVRQIAP GQTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDI STE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTG TG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQ L TPTWRVYSTG SNVFQTRAGC LIGAEHVNNS YECDIPIGAG ICASYQTQTN SPGSASSVAS QSIIAYTMSL GAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKDF GGFNFSQILP DPSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD E MIAQYTSA LLAGTITSGW TFGAGPALQI PFPMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTPSALG KL QDVVNQN AQALNTLVKQ LSSNFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATK MSECVL GQSKRVDFCG KGYHLMSFPQ SAPHGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRN FYEPQ IITTDNTFVS GNCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNE VAKN LNESLIDLQE LGKYEQGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKG GGS GGGGSGGSAW SHPQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60614 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |