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Yorodumi- EMDB-27529: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in com... -
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-Basic information
Entry | Database: EMDB / ID: EMD-27529 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 | |||||||||
Map data | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 | |||||||||
Sample |
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Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy ...Metabolism of Angiotensinogen to Angiotensins / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / endopeptidase activity / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / apical plasma membrane / 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 / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Zhu X / Saville JW / Mannar D / Berezuk AM / Cholak S / Tuttle KS / Vahdatihassani F / Subramaniam S | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: Cell Rep / Year: 2023 Title: Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Authors: James W Saville / Dhiraj Mannar / Xing Zhu / Alison M Berezuk / Spencer Cholak / Katharine S Tuttle / Faezeh Vahdatihassani / Sriram Subramaniam / Abstract: The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages ...The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages threatened the efficacy of vaccine-elicited antibodies and acquired increased binding to several mammalian ACE2 receptors. Cryoelectron microscopy (cryo-EM) analysis of the BA.2 spike (S) glycoprotein in complex with mouse ACE2 (mACE2) identifies BA.1- and BA.2-mutated residues Q493R, N501Y, and Y505H as complementing non-conserved residues between human and mouse ACE2, rationalizing the enhanced S protein-mACE2 interaction for Omicron variants. Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 amino-terminal domain (NTD) reveal a dramatic reorganization of the highly antigenic N1 loop into a β-strand, providing an explanation for decreased binding of the BA.2 S protein to antibodies isolated from BA.1-convalescent patients. Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly evolving Omicron variant landscape. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27529.map.gz | 123.4 MB | EMDB map data format | |
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Header (meta data) | emd-27529-v30.xml emd-27529.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27529_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_27529.png | 107.8 KB | ||
Others | emd_27529_half_map_1.map.gz emd_27529_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27529 | HTTPS FTP |
-Validation report
Summary document | emd_27529_validation.pdf.gz | 888.5 KB | Display | EMDB validaton report |
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Full document | emd_27529_full_validation.pdf.gz | 888.1 KB | Display | |
Data in XML | emd_27529_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_27529_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27529 | HTTPS FTP |
-Related structure data
Related structure data | 8dm7MC 8dm1C 8dm2C 8dm3C 8dm4C 8dm5C 8dm6C 8dm8C 8dm9C 8dmaC 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_27529.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein...
File | emd_27529_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein...
File | emd_27529_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2
Entire | Name: SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2
Supramolecule | Name: SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: SARS-CoV-2 Omicron BA.2 spike protein
Supramolecule | Name: SARS-CoV-2 Omicron BA.2 spike protein / 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: mouse ACE2
Supramolecule | Name: mouse ACE2 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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 / Strain: Omicron BA.2 |
Molecular weight | Theoretical: 142.441812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV ...String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LGRDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIR GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE K |
-Macromolecule #2: Angiotensin-converting enzyme 2
Macromolecule | Name: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 71.795523 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSSSSWLLLS LVAVTTAQSL TEENAKTFLN NFNQEAEDLS YQSSLASWNY NTNITEENAQ KMSEAAAKWS AFYEEQSKTA QSFSLQEIQ TPIIKRQLQA LQQSGSSALS ADKNKQLNTI LNTMSTIYST GKVCNPKNPQ ECLLLEPGLD EIMATSTDYN S RLWAWEGW ...String: MSSSSWLLLS LVAVTTAQSL TEENAKTFLN NFNQEAEDLS YQSSLASWNY NTNITEENAQ KMSEAAAKWS AFYEEQSKTA QSFSLQEIQ TPIIKRQLQA LQQSGSSALS ADKNKQLNTI LNTMSTIYST GKVCNPKNPQ ECLLLEPGLD EIMATSTDYN S RLWAWEGW RAEVGKQLRP LYEEYVVLKN EMARANNYND YGDYWRGDYE AEGADGYNYN RNQLIEDVER TFAEIKPLYE HL HAYVRRK LMDTYPSYIS PTGCLPAHLL GDMWGRFWTN LYPLTVPFAQ KPNIDVTDAM MNQGWDAERI FQEAEKFFVS VGL PHMTQG FWANSMLTEP ADGRKVVCHP TAWDLGHGDF RIKMCTKVTM DNFLTAHHEM GHIQYDMAYA RQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKSIGLLP SDFQEDSETE INFLLKQALT IVGTLPFTYM LEKWRWMVFR GEIPKEQWMK KWWEM KREI VGVVEPLPHD ETYCDPASLF HVSNDYSFIR YYTRTIYQFQ FQEALCQAAK YNGSLHKCDI SNSTEAGQKL LKMLSL GNS EPWTKALENV VGARNMDVKP LLNYFQPLFD WLKEQNRNSF VGWNTEWSPY ADHHHHHH |
-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: 25 / 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |