[English] 日本語
Yorodumi
- EMDB-40711: CryoEM structure of Western equine encephalitis virus VLP in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40711
TitleCryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor
Map dataDensity map of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8.
Sample
  • Complex: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
    • Protein or peptide: DuD1MoD2 chimeric MXRA8
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsWEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / 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 / virion membrane / structural molecule activity / proteolysis / membrane
Similarity search - Function
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 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. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesWestern equine encephalitis virus / Anas platyrhynchos (mallard)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsZimmerman MI / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Cell / Year: 2023
Title: Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8.
Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J ...Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J Adams / Katherine Basore / Bradley M Whitener / Sathvik Palakurty / Hannah G Davis-Adams / Chengqun Sun / Theron Gilliland / James T Earnest / Hongming Ma / Gregory D Ebel / Christian Zmasek / Richard H Scheuermann / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian ...MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian reservoirs. Here, we show that avian, but not mammalian, MXRA8 can act as a receptor for Sindbis, western equine encephalitis (WEEV), and related alphaviruses with avian reservoirs. Structural analysis of duck MXRA8 complexed with WEEV reveals an inverted binding mode compared with mammalian MXRA8 bound to CHIKV. Whereas both domains of mammalian MXRA8 bind CHIKV E1 and E2, only domain 1 of avian MXRA8 engages WEEV E1, and no appreciable contacts are made with WEEV E2. Using these results, we generated a chimeric avian-mammalian MXRA8 decoy-receptor that neutralizes infection of multiple alphaviruses from distinct antigenic groups in vitro and in vivo. Thus, different alphaviruses can bind MXRA8 encoded by different vertebrate classes with distinct engagement modes, which enables development of broad-spectrum inhibitors.
History
DepositionMay 4, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40711.png

Downloads & links

-
Map

FileDownload / File: emd_40711.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 280 pix.
= 336. Å		1.2 Å/pix.
x 280 pix.
= 336. Å		1.2 Å/pix.
x 280 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.66539735 - 0.95607245
Average (Standard dev.)0.00058308063 (±0.016477492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Density half map A of WEEV-VLP in complex...

Fileemd_40711_half_map_1.map
AnnotationDensity half map A of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Density half map B of WEEV-VLP in complex...

Fileemd_40711_half_map_2.map
AnnotationDensity half map B of WEEV-VLP in complex with a chimeric Duck-D1-Mouse-D2 (DuD1-MoD2) MXRA8.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Western equine encephalitis virus VLP in complex with a chimeric ...

EntireName: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
Components
  • Complex: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
    • Protein or peptide: DuD1MoD2 chimeric MXRA8
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Western equine encephalitis virus VLP in complex with a chimeric ...

SupramoleculeName: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 7.45 MDa

-
Macromolecule #1: DuD1MoD2 chimeric MXRA8

MacromoleculeName: DuD1MoD2 chimeric MXRA8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anas platyrhynchos (mallard)
Molecular weightTheoretical: 30.539193 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLNDRQRV VHWDVYSTYY GDNKMERLCD MYSAGDQRVY SSYNQGRIFM PQNAFTDGN FSLVIKDVAE SDGGIYSCNL HHHYCHLYET VKIQLDVTKK AKAAKEYWDG EKAVIVALEG STVMLPCVNR N QIWTERHL ...String:
SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLNDRQRV VHWDVYSTYY GDNKMERLCD MYSAGDQRVY SSYNQGRIFM PQNAFTDGN FSLVIKDVAE SDGGIYSCNL HHHYCHLYET VKIQLDVTKK AKAAKEYWDG EKAVIVALEG STVMLPCVNR N QIWTERHL EEAQQVVHWD RQLPGVSHDR ADRLLDLYAS GERRAYGPPF LRDRVSVNTN AFARGDFSLR IDELERADEG IY SCHLHHH YCGLHERRVF HLQVTEPA

-
Macromolecule #2: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 47.188562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA ...String:
FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMNPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ATNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KANREG HCPVHSHSTT AVLKEATTHV TATGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTR

UniProtKB: Structural polyprotein

-
Macromolecule #3: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 46.171617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH ...String:
ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH RPGPHAYKSY LEEASGEVYI KPPSGKNVTY ECKCGDYSTG IVSTRTKMNG CTKAKQCIAY KRDQTKWVFN SP DLIRHTD HSVQGKLHIP FRLTPTVCPV PLAHTPTVTK WFKGITLHLT ATRPTLLTTR KLGLRADATA EWITGTTSRN FSV GREGLE YVWGNHEPVR VWAQESAPGD PHGWPHEIII HYYHRHPVYT VIVLCGVALA ILVGTASSAA CIAKARRDCL TPYA LAPNA TVPTALAVLC

UniProtKB: Structural polyprotein

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.45 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.01) / Number images used: 431316
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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