[English] 日本語
Yorodumi- PDB-7wt7: SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wt7 | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1) | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Omicron / Spike-Fab complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Wang, X. / Wang, L. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Cell Discov / Year: 2022 Title: A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Authors: Shuo Liu / Zijing Jia / Jianhui Nie / Ziteng Liang / Jingshu Xie / Lei Wang / Li Zhang / Xiangxi Wang / Youchun Wang / Weijin Huang / | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wt7.cif.gz | 629 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wt7.ent.gz | 519.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wt7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7wt7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7wt7_validation.xml.gz | 97 KB | Display | |
Data in CIF | 7wt7_validation.cif.gz | 146.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/7wt7 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/7wt7 | HTTPS FTP |
-Related structure data
Related structure data | 32770MC 7wt8C 7wt9C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 141277.891 Da / Num. of mol.: 3 / Mutation: F817P, A892P, A899P, A942P, K986P, V987P Source method: isolated from a genetically manipulated source Details: Omicron Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
---|
-Antibody , 2 types, 2 molecules HD
#2: Antibody | Mass: 12998.468 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|---|
#3: Antibody | Mass: 11816.036 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Sugars , 3 types, 45 molecules
#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: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1) Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 494849 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|