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Yorodumi- PDB-8ihp: Structure of Semliki Forest virus VLP in complex with the recepto... -
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-Basic information
Entry | Database: PDB / ID: 8ihp | ||||||||||||
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Title | Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Semliki Forest virus / SFV / receptor / complex / VLDLR / glycoprotein | ||||||||||||
Function / homology | Function and homology information reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle / togavirin / positive regulation of dendrite development / dendrite morphogenesis / T=4 icosahedral viral capsid / cargo receptor activity / virion assembly / lipid transport / small molecule binding / apolipoprotein binding / clathrin-coated pit / cholesterol metabolic process / receptor-mediated endocytosis / VLDLR internalisation and degradation / memory / calcium-dependent protein binding / nervous system development / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / receptor complex / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / calcium ion binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / signal transduction / proteolysis / RNA binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Semliki Forest virus Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||
Authors | Cao, D. / Ma, B. / Cao, Z. / Zhang, X. / Xiang, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell / Year: 2023 Title: Structure of Semliki Forest virus in complex with its receptor VLDLR. Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xinzheng Zhang / Ye Xiang / Abstract: Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used ...Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used cryoelectron microscopy to study the structure of SFV in complex with VLDLR. We found that VLDLR binds multiple E1-DIII sites of SFV through its membrane-distal LDLR class A (LA) repeats. Among the LA repeats of the VLDLR, LA3 has the best binding affinity to SFV. The high-resolution structure shows that LA3 binds SFV E1-DIII through a small surface area of 378 Å, with the main interactions at the interface involving salt bridges. Compared with the binding of single LA3s, consecutive LA repeats around LA3 promote synergistic binding to SFV, during which the LAs undergo a rotation, allowing simultaneous key interactions at multiple E1-DIII sites on the virion and enabling the binding of VLDLRs from divergent host species to SFV. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ihp.cif.gz | 701.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ihp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ihp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/8ihp ftp://data.pdbj.org/pub/pdb/validation_reports/ih/8ihp | HTTPS FTP |
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-Related structure data
Related structure data | 35451MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Spike glycoprotein ... , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 46870.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: P03315 #2: Protein | Mass: 47489.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: P03315 |
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-Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 22 molecules CFILMNO
#3: Protein | Mass: 17848.350 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: P03315, togavirin #4: Protein/peptide | Mass: 4361.682 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155 #5: Sugar | ChemComp-NAG / #6: Chemical | |
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-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component | Name: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Semliki Forest virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 651086 / Symmetry type: POINT | ||||||||||||||||||||||||
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