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Yorodumi- PDB-7yd0: SARS-CoV-2 Omicron 1-RBD up spike trimer complexed with two XG005 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yd0 | ||||||
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Title | SARS-CoV-2 Omicron 1-RBD up spike trimer complexed with two XG005 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-COV-2 / Spike / Antibody | ||||||
Function / homology | Function and homology information 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 ...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 / membrane fusion / Attachment and Entry / 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 / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å | ||||||
Authors | Zhan, W.Q. / Zhang, X. / Chen, Z.G. / Sun, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To be Published Title: SARS-CoV-2 Omicron 1-RBD up spike trimer complexed with two XG005 Fab Authors: Zhan, W.Q. / Zhang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yd0.cif.gz | 681.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yd0.ent.gz | 550.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yd0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7yd0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yd0_validation.xml.gz | 106.4 KB | Display | |
Data in CIF | 7yd0_validation.cif.gz | 157.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/7yd0 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/7yd0 | HTTPS FTP |
-Related structure data
Related structure data | 33744MC 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: 142506.000 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Protein | Mass: 23719.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Antibody | Mass: 21603.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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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: Omicron RBD with XG005 / 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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 61 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153541 / Symmetry type: POINT |