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Yorodumi- EMDB-27730: SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affini... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27730 | ||||||||||||
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Title | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
Map data | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
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 / regulation of vasoconstriction / regulation of cardiac conduction ...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 / 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 / negative regulation of signaling receptor activity / Attachment and Entry / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / complement activation, classical pathway / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / antigen binding / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / antibacterial humoral response / regulation of inflammatory response / Maturation of spike protein / endopeptidase activity / 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 / Potential therapeutics for SARS / 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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / blood microparticle / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / 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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | QCRG Structural Biology Consortium / Remesh SG / Merz GE / Brilot AF / Chio U / Verba KA | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Structure / Year: 2023 Title: Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Authors: Soumya G Remesh / Gregory E Merz / Axel F Brilot / Un Seng Chio / Alexandrea N Rizo / Thomas H Pospiech / Irene Lui / Mathew T Laurie / Jeff Glasgow / Chau Q Le / Yun Zhang / Devan Diwanji / ...Authors: Soumya G Remesh / Gregory E Merz / Axel F Brilot / Un Seng Chio / Alexandrea N Rizo / Thomas H Pospiech / Irene Lui / Mathew T Laurie / Jeff Glasgow / Chau Q Le / Yun Zhang / Devan Diwanji / Evelyn Hernandez / Jocelyne Lopez / Hevatib Mehmood / Komal Ishwar Pawar / Sergei Pourmal / Amber M Smith / Fengbo Zhou / / Joseph DeRisi / Tanja Kortemme / Oren S Rosenberg / Anum Glasgow / Kevin K Leung / James A Wells / Kliment A Verba / Abstract: The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor-binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently ...The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor-binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently engineered the SARS-CoV-2 host entry receptor, ACE2, to tightly bind WT-RBD and prevent viral entry into host cells ("receptor traps"). Here we determine cryo-EM structures of our receptor traps in complex with stabilized Spike ectodomain. We develop a multi-model pipeline combining Rosetta protein modeling software and cryo-EM to allow interface energy calculations even at limited resolution and identify interface side chains that allow for high-affinity interactions between our ACE2 receptor traps and Spike-RBD. Our structural analysis provides a mechanistic rationale for the high-affinity (0.53-4.2 nM) binding of our ACE2 receptor traps to Omicron-RBD confirmed with biolayer interferometry measurements. Finally, we show that ACE2 receptor traps potently neutralize Omicron and Delta pseudotyped viruses, providing alternative therapeutic routes to combat this evolving virus. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27730.map.gz | 229.8 MB | EMDB map data format | |
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Header (meta data) | emd-27730-v30.xml emd-27730.xml | 26.8 KB 26.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27730_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_27730.png | 110.8 KB | ||
Masks | emd_27730_msk_1.map | 244.1 MB | Mask map | |
Others | emd_27730_additional_1.map.gz emd_27730_additional_2.map.gz emd_27730_half_map_1.map.gz emd_27730_half_map_2.map.gz | 229.9 MB 219 MB 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27730 | HTTPS FTP |
-Validation report
Summary document | emd_27730_validation.pdf.gz | 799.1 KB | Display | EMDB validaton report |
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Full document | emd_27730_full_validation.pdf.gz | 798.7 KB | Display | |
Data in XML | emd_27730_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_27730_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27730 | HTTPS FTP |
-Related structure data
Related structure data | 8dv1MC 8dv2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27730.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.251 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27730_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity...
File | emd_27730_additional_1.map | ||||||||||||
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Annotation | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity...
File | emd_27730_additional_2.map | ||||||||||||
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Annotation | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity...
File | emd_27730_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity...
File | emd_27730_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Wuhan-hu-1-Spike bound to linker variant of affinity m...
Entire | Name: SARS-CoV-2 Wuhan-hu-1-Spike bound to linker variant of affinity matured ACE2 mimetic CVD432 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Wuhan-hu-1-Spike bound to linker variant of affinity m...
Supramolecule | Name: SARS-CoV-2 Wuhan-hu-1-Spike bound to linker variant of affinity matured ACE2 mimetic CVD432 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Spike glycoprotein
Supramolecule | Name: Spike glycoprotein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chai...
Supramolecule | Name: Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 133.75325 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQ |
-Macromolecule #2: Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chai...
Macromolecule | Name: Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain type: protein_or_peptide / ID: 2 / 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: 110.531703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QSTIEEQAKT FLDFFDSQAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQS TLAQMYPLQE IQNLTVKLQL QALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP GLNEIMANSL DYNERLWAWE SWRSEVGKQL R PLYEEYVV ...String: QSTIEEQAKT FLDFFDSQAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQS TLAQMYPLQE IQNLTVKLQL QALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP GLNEIMANSL DYNERLWAWE SWRSEVGKQL R PLYEEYVV LKNEMARANH YEDYGDYWRG DYEVNGVDGY DYSRGQLIED VEHTFEEIKP LYEHLHAYVR AKLMNAYPSY IS PIGCLPA HLLGDMWGRF WTNLYSLTVP FGQKPNIDVT DAMVDQAWDA QRIFKEAEKF FVSVGLPNMT QGFWENSMLT DPG NVQKAV CHPTAWDLGK GDFRILMCTK VTMDDFLTAH HEMGHIQYDM AYAAQPFLLR NGANEGFHEA VGEIMSLSAA TPKH LKSIG LLSPDFQEDN ETEINFLLKQ ALTIVGTLPF TYMLEKWRWM VFKGEIPKDQ WMKKWWEMKR EIVGVVEPVP HDETY CDPA SLFHVSNDYS FIRYYTRTLY QFQFQEALCQ AAKHEGPLHK CDISNSTEAG QKLFNMLRLG KSEPWTLALE NVVGAK NMN VRPLLNYFEP LFTWLKDQNK NSFVGWSTDW SPYADQSIKV RISLKSALGD KAYEWNDNEM YLFRSSVAYA MRQYFLK VK NQMILFGEED VRVANLKPRI SFNFFVTAPK NVSDIIPRTE VEKAIRMSRS RINDAFRLND NSLEFLGIQP TLGPPNQP P VSGSSGGGGS GGGGEPKSCD KTHTCPPCPA PELLGGPSVF LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVD GVEVHNAKTK PREEQYNSTY RVVSVLTVLH QDWLNGKEYK CKVSNKALPA PIEKTISKAK GQPREPQVYT LPPSRDELTK NQVSLTCLV KGFYPSDIAV EWESNGQPEN NYKTTPPVLD SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK S LSLSPGK |
-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: 7 / 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
Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.0 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 10685 / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |