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- PDB-7ffl: Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 2-fold axes -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ffl | ||||||
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Title | Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 2-fold axes | ||||||
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![]() | VIRUS LIKE PARTICLE/PROTEIN BINDING / Virus / Receptor / Complex / VIRUS LIKE PARTICLE / VIRUS LIKE PARTICLE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() togavirin / regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / symbiont-mediated suppression of host gene expression / amyloid-beta binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity ...togavirin / regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / symbiont-mediated suppression of host gene expression / amyloid-beta binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Zhang, X. / Xiang, Y. / Ma, J. / Ma, B. / Huang, C. | ||||||
![]() | ![]() Title: Structure of Venezuelan equine encephalitis virus with its receptor LDLRAD3. Authors: Bingting Ma / Cuiqing Huang / Jun Ma / Ye Xiang / Xinzheng Zhang / ![]() Abstract: Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available ...Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available that prevent or cure diseases caused by VEEV. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) was recently identified as a receptor for the entry of VEEV into host cells. Here we present the cryo-electron microscopy structure of the LDLRAD3 extracellular domain 1 (LDLRAD3-D1) in complex with VEEV virus-like particles at a resolution of 3.0 Å. LDLRAD3-D1 has a cork-like structure and is inserted into clefts formed between adjacent VEEV E2-E1 heterodimers in the viral-surface trimer spikes through hydrophobic and polar contacts. Mutagenesis studies of LDLRAD3-D1 identified residues that are involved in the key interactions with VEEV. Of note, some of the LDLRAD3-D1 mutants showed a significantly increased binding affinity for VEEV, suggesting that LDLRAD3-D1 may serve as a potential scaffold for the development of inhibitors of VEEV entry. Our structures provide insights into alphavirus assembly and the binding of receptors to alphaviruses, which may guide the development of therapeutic countermeasures against alphaviruses. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 569.4 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 31568MC ![]() 7ffeC ![]() 7fffC ![]() 7ffnC ![]() 7ffoC ![]() 7ffqC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 9 molecules AFSDEHIPT
#1: Protein | Mass: 30980.801 Da / Num. of mol.: 3 / Mutation: K64N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: TC-83 / Production host: ![]() #3: Protein | Mass: 7614.737 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 6488.601 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: TC-83 / Production host: ![]() |
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-Spike glycoprotein ... , 2 types, 6 molecules BCGJQR
#2: Protein | Mass: 47952.066 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: TC-83 / Production host: ![]() #5: Protein | Mass: 47113.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: TC-83 / Production host: ![]() |
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-Non-polymers , 1 types, 3 molecules ![](data/chem/img/CA.gif)
#6: Chemical |
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-Details
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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 894423 / Symmetry type: POINT |