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Yorodumi- PDB-8k9j: SARS-CoV-2 spike protein in complex with two S2H5 Fabs on NTD-1 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k9j | ||||||
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Title | SARS-CoV-2 spike protein in complex with two S2H5 Fabs on NTD-1 and NTD-2 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / coronavirus / spike 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 / 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 2 Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | ||||||
Authors | Hong, Q. / Cong, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Dian Zi Xian Wei Xue Bao / Year: 2024 Title: Molecular basis of SARS-CoV-2 immune evasion of NTD neutralizing antibodies. Authors: Hong, Q. / Xu, S.Q. / Huang, Z. / Cong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k9j.cif.gz | 690.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k9j.ent.gz | 541.6 KB | Display | PDB format |
PDBx/mmJSON format | 8k9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k9j_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8k9j_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8k9j_validation.xml.gz | 113 KB | Display | |
Data in CIF | 8k9j_validation.cif.gz | 168.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/8k9j ftp://data.pdbj.org/pub/pdb/validation_reports/k9/8k9j | HTTPS FTP |
-Related structure data
Related structure data | 36988MC 8k9bC 8k9mC 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: 140055.906 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: Antibody | Mass: 23203.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #3: Antibody | Mass: 24176.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #4: Sugar | ChemComp-NAG / | Has ligand of interest | Y | |
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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 spike protein in complex with S2H5 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
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: 800 nm |
Image recording | Electron dose: 49.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13356 / Symmetry type: POINT | ||||||||||||||||||||||||
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