[English] 日本語
![](img/lk-miru.gif)
- PDB-5w9i: MERS S ectodomain trimer in complex with variable domain of neutr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5w9i | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 | |||||||||
![]() |
| |||||||||
![]() | VIRAL PROTEIN / Immunogen / peplomer / viral spike / MERS / MERS S protein / antibody / G4 | |||||||||
Function / homology | ![]() endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Pallesen, J. / Ward, A.B. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing- ...Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing-Pui Kong / Erica L Andres / Arminja N Kettenbach / Mark R Denison / James D Chappell / Barney S Graham / Andrew B Ward / Jason S McLellan / ![]() Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 731.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 553.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8784MC ![]() 8783C ![]() 8785C ![]() 8786C ![]() 8787C ![]() 8788C ![]() 8789C ![]() 8790C ![]() 8791C ![]() 8792C ![]() 8793C ![]() 5vyhC ![]() 5vzrC ![]() 5w9hC ![]() 5w9jC ![]() 5w9kC ![]() 5w9lC ![]() 5w9mC ![]() 5w9nC ![]() 5w9oC ![]() 5w9pC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 146325.969 Da / Num. of mol.: 6 / Mutation: V1060P, L1061P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() #2: Antibody | Mass: 25312.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23867.367 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | 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: Sugar | ChemComp-NAG / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: MERS S ectodomain trimer in complex with Fab of neutralizing antibody G4 Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Buffer component | Name: TBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.89 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Sampling size: 5 µm / Movie frames/image: 35 / Used frames/image: 1-35 |
-
Processing
Software | Name: PHENIX / Version: 1.11.1_2580: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 37180 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37180 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|