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- EMDB-27272: CryoEM structure of Western equine encephalitis virus VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-27272
TitleCryoEM structure of Western equine encephalitis virus VLP
Map dataMap of WEEV-VLP asymmetric unit
Sample
  • Virus: Western equine encephalitis virus
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsWEEV / Alphavirus / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE
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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsZimmerman MI / Fremont DH
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 repeat domain 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
DepositionJun 13, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27272.png

Downloads & links

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Map

FileDownload / File: emd_27272.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of WEEV-VLP asymmetric unit
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: 0.45
Minimum - Maximum-0.8452039 - 1.6331984
Average (Standard dev.)0.003849539 (±0.054169204)
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: Half-map A

Fileemd_27272_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_27272_half_map_2.map
AnnotationHalf-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 : Western equine encephalitis virus

EntireName: Western equine encephalitis virus
Components
  • Virus: Western equine encephalitis virus
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 440062
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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