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- EMDB-64199: CryoEM structure of Western equine encephalitis virus California ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64199
TitleCryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LA1-3
Map data
Sample
  • Virus: Western equine encephalitis virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION
KeywordsWEEV / VLP / E2-E1 glycoproteins / 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-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / 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
Similarity search - Component
Biological speciesWestern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLiang SJ / Lou ZY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural insights into VLDLR recognition by Western Equine Encephalitis Virus
Authors: Liang SJ / Lou ZY
History
DepositionApr 15, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64199.png

Downloads & links

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Map

FileDownload / File: emd_64199.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.22333345 - 18.369129999999998
Average (Standard dev.)0.194874 (±0.99541616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64199_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64199_half_map_2.map
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: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION

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Supramolecule #1: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 47.390863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA ...String:
FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMKPG AFGDIQASSL YATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ASNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KADREG HCPVHSHSTT AVLKEATTHV TATGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTRR

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: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 46.534066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL LKCHIYDHLK E TSAGYITM ...String:
SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL LKCHIYDHLK E TSAGYITM HRPGPHAYKS YLKEASGEVY IKPPSGKNVT YECKCGDYST GIVSTQTKMN GCTKARQCIA YTRDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCR VPLAHTPTVT KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPY ALAPN ATVPTALAVL CCI

UniProtKB: Structural polyprotein

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Macromolecule #3: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.783614 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KCEPSQFQCT NGRCITLLWK CDGDEDCVDG SDEKNCVKKT CAESDFVCNN GQCVPSRWKC DGDPDCEDGS DESPEQCHM

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

27389

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139762
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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