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- EMDB-28644: CryoEM structure of Western equine encephalitis virus VLP in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-28644
TitleCryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor
Map dataChikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8.
Sample
  • Complex: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
    • Protein or peptide: E1 envelope protein
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
  • 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 / VIRUS LIKE PARTICLE / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / 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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus / Anas platyrhynchos (mallard)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 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: To Be Published
Title: Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion
Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C ...Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C / Scheuermann RH / Fremont DH / Diamond MS
History
DepositionOct 22, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28644.png

Downloads & links

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Map

FileDownload / File: emd_28644.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse 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: 0.16
Minimum - Maximum-0.22509056 - 0.8991995
Average (Standard dev.)0.0024239735 (±0.03958594)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: Chikungunya virus-like particle (CHIKV VLP) in complex with...

Fileemd_28644_half_map_1.map
AnnotationChikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. Half-map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Chikungunya virus-like particle (CHIKV VLP) in complex with...

Fileemd_28644_half_map_2.map
AnnotationChikungunya virus-like particle (CHIKV VLP) in complex with a designed MXRA8, a chimera containing D1 from Duck MXRA8 and D2 from Mouse MXRA8. Half-map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (...

EntireName: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
Components
  • Complex: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
    • Protein or peptide: E1 envelope protein
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (...

SupramoleculeName: Chikungunya 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: Chikungunya virus
Molecular weightTheoretical: 495 kDa/nm

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Macromolecule #1: E1 envelope protein

MacromoleculeName: E1 envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 47.346715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNIP ISIDIPDAAF TRVVDAPSVT DMSCEVPACT HSSDFGGVAI IKY TASKKG KCAVHSMTNA VTIREADVEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAACHPPKDH IVNYPASHTT LGVQ DISTT AMSWVQKITG GVGLIVAVAA LILIVVLCVS FSRH

UniProtKB: Structural polyprotein

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Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 46.858312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP ...String:
NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP PDTPDRTLMT QQSGNVKITV NGQTVRYKCN CGGSNEGLTT TDKVINNCKI DQCHAAVTNH KNWQYNSPLV PR NAELGDR KGKIHIPFPL ANVTCRVPKA RNPTVTYGKN QVTMLLYPDH PTLLSYRNMG QEPNYHEEWV THKKEVTLTV PTE GLEVTW GNNEPYKYWP QMSTNGTAHG HPHEIILYYY ELYPTMTVVI VSVASFVLLS MVGTAVGMCV CARRRCITPY ELTP GATVP FLLSLLCCVR TTKA

UniProtKB: Structural polyprotein

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Macromolecule #3: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8

MacromoleculeName: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
type: protein_or_peptide / ID: 3 / 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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.03 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

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.01) / Number images used: 745448
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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