[English] 日本語
Yorodumi
- PDB-8ys2: Overall structure of Eastern Equine Encephalitis virus VLP in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ys2
TitleOverall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor VLDLR LA1-2
Components
  • Capsid protein
  • Spike glycoprotein E1
  • Spike glycoprotein E2
  • Very low-density lipoprotein receptor
KeywordsVIRUS LIKE PARTICLE / Eastern Equine Encephalitis virus / EEEV / receptor / complex / VLDLR / glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway ...reelin receptor activity / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / togavirin / very-low-density lipoprotein particle / positive regulation of dendrite development / T=4 icosahedral viral capsid / cargo receptor activity / dendrite morphogenesis / lipid transport / apolipoprotein binding / clathrin-coated pit / cholesterol metabolic process / VLDLR internalisation and degradation / receptor-mediated endocytosis / memory / symbiont-mediated suppression of host gene expression / calcium-dependent protein binding / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / receptor complex / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / signal transduction / proteolysis / RNA binding / membrane / plasma membrane
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / : / Calcium-binding EGF domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Very low-density lipoprotein receptor / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsCao, D. / Ma, B. / Cao, Z. / Xu, X. / Zhang, X. / Xiang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xiaoyu Xu / Xinzheng Zhang / Ye Xiang /
Abstract: Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of ...Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of EEEV. Herein, we performed cryo-electron microscopy structural and biochemistry studies on the specific interactions between EEEV and VLDLR. Our results show that VLDLR binds EEEV at three different sites A, B and C through its membrane-distal LDLR class A (LA) repeats. Site A is located in the cleft in between the E1-E2 heterodimers. Site B is located near the connecting β ribbon of E2 and is in proximity to site A, while site C is on the domain B of E2. The binding of VLDLR LAs to EEEV is in complex modes, including the LA1-2 and LA3-5 mediated two major modes. Disruption of the LA1-2 mediated binding significantly affect the cell attachment of EEEV. However, the mutation W132G of VLDLR impairs the binding of LA3, drives the switch of the binding modes, and significantly enhances the attachment of EEEV to the cell. The W132G variant of VLDLR could be identified in human genome and SNP sequences, implying that people with similar mutations in VLDLR may be highly susceptible to EEEV infection.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Capsid protein
D: Spike glycoprotein E1
E: Spike glycoprotein E2
F: Capsid protein
G: Spike glycoprotein E1
H: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
L: Capsid protein
M: Very low-density lipoprotein receptor
N: Very low-density lipoprotein receptor
O: Very low-density lipoprotein receptor
P: Very low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,58024
Polymers532,25916
Non-polymers3218
Water00
1
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Capsid protein
D: Spike glycoprotein E1
E: Spike glycoprotein E2
F: Capsid protein
G: Spike glycoprotein E1
H: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
L: Capsid protein
M: Very low-density lipoprotein receptor
N: Very low-density lipoprotein receptor
O: Very low-density lipoprotein receptor
P: Very low-density lipoprotein receptor
hetero molecules
x 60


  • defined by author&software
  • Evidence: electron microscopy, not applicable
  • 32 MDa, 960 polymers
Theoretical massNumber of molelcules
Total (without water)31,954,7901440
Polymers31,935,553960
Non-polymers19,237480
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

-
Components

#1: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 47984.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7
#2: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 47047.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7
#3: Protein
Capsid protein / Coat protein / C


Mass: 29178.846 Da / Num. of mol.: 4 / Mutation: K67N
Source method: isolated from a genetically manipulated source
Details: AAU95735.1 / Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7, togavirin
#4: Protein
Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 8854.691 Da / Num. of mol.: 4
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Eastern equine encephalitis virus / Type: VIRUS
Details: EEEV Virus like particle in complexed with its receptor VLDLR LA1-2
Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Eastern equine encephalitis virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Eastern equine encephalitis virus
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15654 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334658
ELECTRON MICROSCOPYf_angle_d0.73347213
ELECTRON MICROSCOPYf_dihedral_angle_d8.3724708
ELECTRON MICROSCOPYf_chiral_restr0.0495223
ELECTRON MICROSCOPYf_plane_restr0.0076124

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more