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Yorodumi- PDB-8vkm: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vkm | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 1) | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / negative regulation of smooth muscle cell proliferation / brush border membrane / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / virus receptor activity / endopeptidase activity / 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 / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 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, T.S. / Subramaniam, S. | ||||||
Funding support | Canada, 1items
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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, T.S. / Subramaniam, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vkm.cif.gz | 940.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vkm.ent.gz | 618.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vkm_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8vkm_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8vkm_validation.xml.gz | 107.4 KB | Display | |
Data in CIF | 8vkm_validation.cif.gz | 163.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/8vkm ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vkm | HTTPS FTP |
-Related structure data
Related structure data | 43322MC 8vkkC 8vklC 8vknC 8vkoC 8vkpC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 142226.516 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Protein | | Mass: 71795.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ace2 / Production host: Homo sapiens (human) References: UniProt: Q8R0I0, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SARS-CoV-2 XBB.1.5 spike protein trimer bound to mouse ACE2 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61334 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.03 Å2 | ||||||||||||||||||||||||
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