[English] 日本語
Yorodumi- PDB-7n1h: CryoEM structure of Venezuelan equine encephalitis virus VLP in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n1h | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor | ||||||
Components |
| ||||||
Keywords | VIRUS LIKE PARTICLE / VEEV / viral envelope / host receptor / low-density lipoprotein receptor type-A module / LDLRAD3 / encephalitic alphavirus / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell ...regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Venezuelan equine encephalitis virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Basore, K. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nature / Year: 2021 Title: Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor. Authors: Katherine Basore / Hongming Ma / Natasha M Kafai / Samantha Mackin / Arthur S Kim / Christopher A Nelson / Michael S Diamond / Daved H Fremont / Abstract: LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present ...LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present near-atomic-resolution cryo-electron microscopy reconstructions of VEEV virus-like particles alone and in a complex with the ectodomains of LDLRAD3. Domain 1 of LDLRAD3 is a low-density lipoprotein receptor type-A module that binds to VEEV by wedging into a cleft created by two adjacent E2-E1 heterodimers in one trimeric spike, and engages domains A and B of E2 and the fusion loop in E1. Atomic modelling of this interface is supported by mutagenesis and anti-VEEV antibody binding competition assays. Notably, VEEV engages LDLRAD3 in a manner that is similar to the way that arthritogenic alphaviruses bind to the structurally unrelated MXRA8 receptor, but with a much smaller interface. These studies further elucidate the structural basis of alphavirus-receptor interactions, which could inform the development of therapies to mitigate infection and disease against multiple members of this family. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7n1h.cif.gz | 726.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7n1h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7n1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n1h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7n1h_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7n1h_validation.xml.gz | 138.9 KB | Display | |
Data in CIF | 7n1h_validation.cif.gz | 204.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/7n1h ftp://data.pdbj.org/pub/pdb/validation_reports/n1/7n1h | HTTPS FTP |
-Related structure data
Related structure data | 24116MC 7n1iC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 3 types, 12 molecules DCBAHGFELKJI
#2: Protein | Mass: 47952.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98 #3: Protein | Mass: 47113.746 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98 #4: Protein | Mass: 18195.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98 |
---|
-Protein/peptide / Non-polymers / Sugars , 3 types, 16 molecules OMNP
#1: Protein/peptide | Mass: 4312.861 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldlrad3 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A2AR95 #5: Chemical | ChemComp-CA / #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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||||||||||
Natural host | Organism: Mosquito | ||||||||||||||||||||||||||||
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12216 / Symmetry type: POINT |