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Yorodumi- PDB-7zjl: Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zjl | ||||||
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Title | Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue. | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / REGN10987 / Fab / cryo-EM / S-protein | ||||||
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 / 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 / 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 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Pichkur, E.B. / Lyukmanova, E.N. / Shenkarev, Z.O. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue. Authors: Pichkur, E.B. / Lyukmanova, E.N. / Shenkarev, Z.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zjl.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zjl.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7zjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zjl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zjl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7zjl_validation.xml.gz | 117.7 KB | Display | |
Data in CIF | 7zjl_validation.cif.gz | 185.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zjl ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zjl | HTTPS FTP |
-Related structure data
Related structure data | 14750MC 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: 125147.805 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 / Cell line (production host): Hek293 Expi cells / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 23334.691 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 23792.617 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: 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 |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: 20 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44323 Details: FSC is reported for C1 map after global refinement and doesn't represent the resolution of the RBD-FAB areas. Symmetry type: POINT |