National Natural Science Foundation of China (NSFC)
China
Chinese Academy of Sciences
China
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.
Entire : Semliki Forest virus VLP in complex with its receptor VLDLR at th...
Entire
Name: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
Components
Complex: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
Protein or peptide: Spike glycoprotein E2
Protein or peptide: Spike glycoprotein E1
Protein or peptide: Capsid proteinCapsid
Protein or peptide: Very low-density lipoprotein receptor
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Ligand: CALCIUM IONCalcium
-
Supramolecule #1: Semliki Forest virus VLP in complex with its receptor VLDLR at th...
Supramolecule
Name: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)
Organism: Semliki Forest virus
-
Macromolecule #1: Spike glycoprotein E2
Macromolecule
Name: Spike glycoprotein E2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi