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- EMDB-47119: Structure of western equine encephalitis virus McMillan VLP in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-47119
TitleStructure of western equine encephalitis virus McMillan VLP in complex with human VLDLR
Map data
Sample
  • Complex: western equine encephalitis virus McMillan VLP in complex with human VLDLR
    • Complex: western equine encephalitis virus McMillan VLP
      • Protein or peptide: Capsid protein
    • Complex: Very low-density lipoprotein receptor
      • Protein or peptide: Very low-density lipoprotein receptor
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Structural polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordswestern equine encephalitis virus / WEEV / receptor binding / VLDLR / virus like particles / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / 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 / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / 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 / cargo receptor activity / T=4 icosahedral viral capsid / positive regulation of dendrite development / dendrite morphogenesis / lipid transport / regulation of synapse assembly / apolipoprotein binding / clathrin-coated pit / receptor-mediated endocytosis / cholesterol metabolic process / VLDLR internalisation and degradation / memory / calcium-dependent protein binding / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / receptor complex / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / glutamatergic synapse / structural molecule activity / 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. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / 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
Structural polyprotein / Structural polyprotein / Very low-density lipoprotein receptor / Structural polyprotein
Similarity search - Component
Biological speciesWestern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAbraham J / Fan X / Li W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR
Authors: Abraham J / Fan X / Li W
History
DepositionSep 24, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47119.png

Downloads & links

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Map

FileDownload / File: emd_47119.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0026694587 - 1.9559143
Average (Standard dev.)0.008933512 (±0.059098072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47119_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_47119_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 McMillan VLP in complex with hu...

EntireName: western equine encephalitis virus McMillan VLP in complex with human VLDLR
Components
  • Complex: western equine encephalitis virus McMillan VLP in complex with human VLDLR
    • Complex: western equine encephalitis virus McMillan VLP
      • Protein or peptide: Capsid protein
    • Complex: Very low-density lipoprotein receptor
      • Protein or peptide: Very low-density lipoprotein receptor
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Structural polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: western equine encephalitis virus McMillan VLP in complex with hu...

SupramoleculeName: western equine encephalitis virus McMillan VLP in complex with human VLDLR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4
Source (natural)Organism: Western equine encephalitis virus

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Supramolecule #2: western equine encephalitis virus McMillan VLP

SupramoleculeName: western equine encephalitis virus McMillan VLP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Western equine encephalitis virus

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Supramolecule #3: Very low-density lipoprotein receptor

SupramoleculeName: Very low-density lipoprotein receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 47.185582 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 DATDIVARTD 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 NTR

UniProtKB: Structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 45.550859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVQGKL VKCHVYDRLK E TSAGYITM ...String:
SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVQGKL VKCHVYDRLK E TSAGYITM HRPGPHAYKS YLKEASGEVY IKPPSGKNVT YECKCGDYST GIVSTQTKMN GCTKARQCIA YKLDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCP VPLAHTPTVT KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPY ALAPN ATVP

UniProtKB: Structural polyprotein

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 17.320688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MCMKLESDKT FPIMLNGQVN GYACVVGGRL MKPLHVEGKI DNEQLAAVKL KKASMYDLEY GDVPQNMKSD TLQYTSDKPP GFYNWHHGA VQYENGRFTV PRGVGGKGDS GRPILDNRGR VVAIVLGGAN EGTRTALSVV TWNQKGVTIK DTPEGSEPW

UniProtKB: Structural polyprotein

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Macromolecule #4: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.654436 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CEPSQFQCTN GRCITLLWKC DGDEDCVDGS DEKNCVKKTC AESDFVCNNG QCVPSRWKCD GDPDCEDGSD ESPEQCHM

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 0.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5210

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72772
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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