[English] 日本語
Yorodumi- PDB-7sww: SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sww | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (local refinement) | |||||||||
Components |
| |||||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Glycoprotein / Antibody / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN-IMMUNE SYSTEM complex / Center for Structural Biology of Infectious Diseases / CSBID | |||||||||
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 Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Adams, L.J. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID) | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To Be Published Title: A protective antibody targeting the N-terminal domain of SARS-CoV-2 spike recognizes most emerging variants Authors: Adams, L.J. / VanBlargan, L.A. / Liu, Z. / Gilchuk, P. / Zhao, H. / Chen, R.E. / Raju, S. / Whitener, B. / Shrihari, S. / Jethva, P.N. / Gross, M.L. / Crowe, J.E. / Whelan, S.P.J. / Diamond, M.S. / Fremont, D.H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7sww.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7sww.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 7sww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sww_validation.pdf.gz | 787.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7sww_full_validation.pdf.gz | 793.9 KB | Display | |
Data in XML | 7sww_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 7sww_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/7sww ftp://data.pdbj.org/pub/pdb/validation_reports/sw/7sww | HTTPS FTP |
-Related structure data
Related structure data | 25487MC 7swxC 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
#1: Protein | Mass: 33082.352 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 14-304) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 12955.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
#3: Antibody | Mass: 12383.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / 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 spike bound by SARS2-57 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
---|---|
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
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 |
Image recording | Electron dose: 66.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4379: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241481 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|