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Yorodumi- EMDB-43323: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43323 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (focused refinement of RBD and mouse ACE2) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / 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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of cardiac conduction ...Metabolism of Angiotensinogen to Angiotensins / 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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / metallocarboxypeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / 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 / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / extracellular region / membrane / identical protein binding / 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: 2.93 Å | |||||||||
Authors | Zhu X / Mannar D / Saville J / Poloni C / Bezeruk A / Tidey K / Ahmed S / Tuttle K / Vahdatihassani F / Cholak S ...Zhu X / Mannar D / Saville J / Poloni C / Bezeruk A / Tidey K / Ahmed S / Tuttle K / Vahdatihassani F / Cholak S / Cook L / Steiner TS / Subramaniam S | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: To Be Published Title: SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition Authors: Mannar D / Saville J / Poloni C / Zhu X / Bezeruk A / Tidey K / Ahmed S / Tuttle K / Vahdatihassani F / Cholak S / Cook L / Steiner TS / Subramaniam S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43323.map.gz | 123.1 MB | EMDB map data format | |
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Header (meta data) | emd-43323-v30.xml emd-43323.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43323_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_43323.png | 18.3 KB | ||
Filedesc metadata | emd-43323.cif.gz | 6 KB | ||
Others | emd_43323_half_map_1.map.gz emd_43323_half_map_2.map.gz | 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43323 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43323 | HTTPS FTP |
-Related structure data
Related structure data | 8vknMC 8vkkC 8vklC 8vkmC 8vkoC 8vkpC 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_43323.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #1
File | emd_43323_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43323_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 XBB.1.5 spike protein RBD bound to mouse ACE2
Entire | Name: SARS-CoV-2 XBB.1.5 spike protein RBD bound to mouse ACE2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 XBB.1.5 spike protein RBD bound to mouse ACE2
Supramolecule | Name: SARS-CoV-2 XBB.1.5 spike protein RBD bound to mouse ACE2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Details: XBB.1.5 RBD / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.580527 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLFRK SKLKPFERDI STEIYQAGNK PCNGVAGPNC Y SPLQSYGF ...String: PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLFRK SKLKPFERDI STEIYQAGNK PCNGVAGPNC Y SPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKS UniProtKB: Spike glycoprotein |
-Macromolecule #2: Angiotensin-converting enzyme 2
Macromolecule | Name: Angiotensin-converting enzyme 2 / 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: 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 UniProtKB: Angiotensin-converting enzyme 2 |
-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: 1 / 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |