+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23156 | |||||||||
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Title | SARS-CoV 2 Spike Protein bound to LY-CoV555 | |||||||||
Map data | Unsharpened map for SARS-CoV-2 Spike protein bound to LY-CoV555 | |||||||||
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 / 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 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Goldsmith JA / McLellan JS | |||||||||
Citation | Journal: bioRxiv / Year: 2020 Title: LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection. Authors: Bryan E Jones / Patricia L Brown-Augsburger / Kizzmekia S Corbett / Kathryn Westendorf / Julian Davies / Thomas P Cujec / Christopher M Wiethoff / Jamie L Blackbourne / Beverly A Heinz / ...Authors: Bryan E Jones / Patricia L Brown-Augsburger / Kizzmekia S Corbett / Kathryn Westendorf / Julian Davies / Thomas P Cujec / Christopher M Wiethoff / Jamie L Blackbourne / Beverly A Heinz / Denisa Foster / Richard E Higgs / Deepa Balasubramaniam / Lingshu Wang / Roza Bidshahri / Lucas Kraft / Yuri Hwang / Stefanie Žentelis / Kevin R Jepson / Rodrigo Goya / Maia A Smith / David W Collins / Samuel J Hinshaw / Sean A Tycho / Davide Pellacani / Ping Xiang / Krithika Muthuraman / Solmaz Sobhanifar / Marissa H Piper / Franz J Triana / Jorg Hendle / Anna Pustilnik / Andrew C Adams / Shawn J Berens / Ralph S Baric / David R Martinez / Robert W Cross / Thomas W Geisbert / Viktoriya Borisevich / Olubukola Abiona / Hayley M Belli / Maren de Vries / Adil Mohamed / Meike Dittmann / Marie Samanovic / Mark J Mulligan / Jory A Goldsmith / Ching-Lin Hsieh / Nicole V Johnson / Daniel Wrapp / Jason S McLellan / Bryan C Barnhart / Barney S Graham / John R Mascola / Carl L Hansen / Ester Falconer Abstract: SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the ...SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection. ONE SENTENCE SUMMARY: LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates ...ONE SENTENCE SUMMARY: LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates against SARS-CoV-2 infection. | |||||||||
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_23156.map.gz | 154.1 MB | EMDB map data format | |
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Header (meta data) | emd-23156-v30.xml emd-23156.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23156_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_23156.png | 117.1 KB | ||
Others | emd_23156_additional_1.map.gz emd_23156_half_map_1.map.gz emd_23156_half_map_2.map.gz | 288.6 MB 285.1 MB 285.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23156 | HTTPS FTP |
-Validation report
Summary document | emd_23156_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_23156_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_23156_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_23156_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23156 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23156 | HTTPS FTP |
-Related structure data
Related structure data | 7l3nMC 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_23156.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened map for SARS-CoV-2 Spike protein bound to LY-CoV555 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: LocalDeBlur sharpened map for SARS-CoV-2 Spike protein bound...
File | emd_23156_additional_1.map | ||||||||||||
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Annotation | LocalDeBlur sharpened map for SARS-CoV-2 Spike protein bound to LY-CoV555 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A for SARS-CoV-2 Spike protein bound to LY-CoV555
File | emd_23156_half_map_1.map | ||||||||||||
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Annotation | Half map A for SARS-CoV-2 Spike protein bound to LY-CoV555 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B for SARS-CoV-2 Spike protein bound to LY-CoV555
File | emd_23156_half_map_2.map | ||||||||||||
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Annotation | Half map B for SARS-CoV-2 Spike protein bound to LY-CoV555 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike protein bound to neutralizing antibody LY-CoV555
Entire | Name: SARS-CoV-2 spike protein bound to neutralizing antibody LY-CoV555 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike protein bound to neutralizing antibody LY-CoV555
Supramolecule | Name: SARS-CoV-2 spike protein bound to neutralizing antibody LY-CoV555 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: SARS-CoV-2 spike protein
Supramolecule | Name: SARS-CoV-2 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: neutralizing antibody LY-CoV555
Supramolecule | Name: neutralizing antibody LY-CoV555 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-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: 141.067672 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SQCVNLTTRT QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV S QPFLMDLE ...String: SQCVNLTTRT QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV S QPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PG DSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQPTESIVRF PNI TNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAP GQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS TPCNGVEGFN CYFPL QSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTESN KKFLPFQQFG RDIADT TDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQDV NCTEVPVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIG AE HVNNSYECDI PIGAGICASY QTQTNSPGSA SSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMT K TSVDCTMYIC GDSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNFS QILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAGP ALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNQNAQALNT LVKQLSSNFG A ISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SF PQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFVSGNCDVV IGI VNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ GSGY IPEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWSHPQFE K |
-Macromolecule #2: LY-CoV555 Fab heavy chain
Macromolecule | Name: LY-CoV555 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.669691 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS NYAISWVRQA PGQGLEWMGR IIPILGIANY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCARG YYEARHYYYY YAMDVWGQGT AVTVSSASTK GPSVFPLAPC SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS NYAISWVRQA PGQGLEWMGR IIPILGIANY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCARG YYEARHYYYY YAMDVWGQGT AVTVSSASTK GPSVFPLAPC SRSTSESTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTKTYTC NVDHKPSNTK VDKRVHHHHH |
-Macromolecule #3: LY-CoV555 Fab light chain
Macromolecule | Name: LY-CoV555 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.097557 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLSWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ QSYSTPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLSWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ QSYSTPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTQ GTTSVTKSFN RGEC |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 16 / 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 | 2D array |
-Sample preparation
Buffer | pH: 8 |
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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) / Average electron dose: 37.2 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 |