+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12187 | |||||||||
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Title | SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain | |||||||||
Map data | SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / negative regulation of signaling receptor activity / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / negative regulation of signaling receptor activity / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of inflammatory response / regulation of cell population proliferation / endopeptidase activity / Potential therapeutics for SARS / 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 / apical plasma membrane / symbiont entry into host cell / membrane raft / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Elad N / Dym O / Zahradnik J / Schreiber G | |||||||||
Funding support | Israel, 2 items
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Citation | Journal: Nat Microbiol / Year: 2021 Title: SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Authors: Jiří Zahradník / Shir Marciano / Maya Shemesh / Eyal Zoler / Daniel Harari / Jeanne Chiaravalli / Björn Meyer / Yinon Rudich / Chunlin Li / Ira Marton / Orly Dym / Nadav Elad / Mark G ...Authors: Jiří Zahradník / Shir Marciano / Maya Shemesh / Eyal Zoler / Daniel Harari / Jeanne Chiaravalli / Björn Meyer / Yinon Rudich / Chunlin Li / Ira Marton / Orly Dym / Nadav Elad / Mark G Lewis / Hanne Andersen / Matthew Gagne / Robert A Seder / Daniel C Douek / Gideon Schreiber / Abstract: SARS-CoV-2 variants of interest and concern will continue to emerge for the duration of the COVID-19 pandemic. To map mutations in the receptor-binding domain (RBD) of the spike protein that affect ...SARS-CoV-2 variants of interest and concern will continue to emerge for the duration of the COVID-19 pandemic. To map mutations in the receptor-binding domain (RBD) of the spike protein that affect binding to angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, we applied in vitro evolution to affinity-mature the RBD. Multiple rounds of random mutagenic libraries of the RBD were sorted against decreasing concentrations of ACE2, resulting in the selection of higher affinity RBD binders. We found that mutations present in more transmissible viruses (S477N, E484K and N501Y) were preferentially selected in our high-throughput screen. Evolved RBD mutants include prominently the amino acid substitutions found in the RBDs of B.1.620, B.1.1.7 (Alpha), B1.351 (Beta) and P.1 (Gamma) variants. Moreover, the incidence of RBD mutations in the population as presented in the GISAID database (April 2021) is positively correlated with increased binding affinity to ACE2. Further in vitro evolution increased binding by 1,000-fold and identified mutations that may be more infectious if they evolve in the circulating viral population, for example, Q498R is epistatic to N501Y. We show that our high-affinity variant RBD-62 can be used as a drug to inhibit infection with SARS-CoV-2 and variants Alpha, Beta and Gamma in vitro. In a model of SARS-CoV-2 challenge in hamster, RBD-62 significantly reduced clinical disease when administered before or after infection. A 2.9 Å cryo-electron microscopy structure of the high-affinity complex of RBD-62 and ACE2, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies. | |||||||||
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_12187.map.gz | 139.2 MB | EMDB map data format | |
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Header (meta data) | emd-12187-v30.xml emd-12187.xml | 23 KB 23 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12187_fsc.xml | 25.6 KB | Display | FSC data file |
Images | emd_12187.png | 141.1 KB | ||
Others | emd_12187_additional_1.map.gz emd_12187_half_map_1.map.gz emd_12187_half_map_2.map.gz | 139.4 MB 139.3 MB 139.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12187 | HTTPS FTP |
-Validation report
Summary document | emd_12187_validation.pdf.gz | 453.5 KB | Display | EMDB validaton report |
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Full document | emd_12187_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | emd_12187_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | emd_12187_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12187 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12187 | HTTPS FTP |
-Related structure data
Related structure data | 7bh9MC 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_12187.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.529 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened map, B-factor of -83
File | emd_12187_additional_1.map | ||||||||||||
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Annotation | Sharpened map, B-factor of -83 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12187_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12187_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Entire | Name: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain |
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Components |
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-Supramolecule #1: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain
Supramolecule | Name: SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: ACE2 extracellular peptidase domain
Supramolecule | Name: ACE2 extracellular peptidase domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: SARS-CoV-2 receptor binding domain
Supramolecule | Name: SARS-CoV-2 receptor binding domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Angiotensin-converting enzyme 2
Macromolecule | Name: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 70.486039 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GSSTIEEQAK TFLDKFNHEA EDLFYQSSLA SWNYNTNITE ENVQNMNNAG DKWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGS SVLSEDKSKR LNTILNTMST IYSTGKVCNP DNPQECLLLE PGLNEIMANS LDYNERLWAW ESWRSEVGKQ L RPLYEEYV ...String: GSSTIEEQAK TFLDKFNHEA EDLFYQSSLA SWNYNTNITE ENVQNMNNAG DKWSAFLKEQ STLAQMYPLQ EIQNLTVKLQ LQALQQNGS SVLSEDKSKR LNTILNTMST IYSTGKVCNP DNPQECLLLE PGLNEIMANS LDYNERLWAW ESWRSEVGKQ L RPLYEEYV VLKNEMARAN HYEDYGDYWR GDYEVNGVDG YDYSRGQLIE DVEHTFEEIK PLYEHLHAYV RAKLMNAYPS YI SPIGCLP AHLLGDMWGR FWTNLYSLTV PFGQKPNIDV TDAMVDQAWD AQRIFKEAEK FFVSVGLPNM TQGFWENSML TDP GNVQKA VCHPTAWDLG KGDFRILMCT KVTMDDFLTA HHEMGHIQYD MAYAAQPFLL RNGANEGFHE AVGEIMSLSA ATPK HLKSI GLLSPDFQED NETEINFLLK QALTIVGTLP FTYMLEKWRW MVFKGEIPKD QWMKKWWEMK REIVGVVEPV PHDET YCDP ASLFHVSNDY SFIRYYTRTL YQFQFQEALC QAAKHEGPLH KCDISNSTEA GQKLFNMLRL GKSEPWTLAL ENVVGA KNM NVRPLLNYFE PLFTWLKDQN KNSFVGWSTD WSPYADGGSG THHHHHH |
-Macromolecule #2: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 2 / Details: SARS-CoV-2 receptor binding domain / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 23.033965 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRFSNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKKGGNYNY LYRLFRKSKL KPFERDTSME IYQAGNTPCN GVKGFNCYFP L QSYGFRPT ...String: TNLCPFGEVF NATRFASVYA WNRKRFSNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKKGGNYNY LYRLFRKSKL KPFERDTSME IYQAGNTPCN GVKGFNCYFP L QSYGFRPT YGVGYQPYRV VVLSFELLHA PATVCGPKHH HHHH |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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 | particle |
-Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4470 / Average exposure time: 1.214 sec. / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 94518 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |