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- EMDB-47846: RRV DKTA VLP in complex with VLDLR-LBD-Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-47846
TitleRRV DKTA VLP in complex with VLDLR-LBD-Fc
Map data
Sample
  • Virus: Ross river virus (STRAIN T48)
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION
KeywordsAlphavirus Receptor / VIRAL PROTEIN
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 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 speciesRoss river virus (STRAIN T48) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsRaju S / Diamond MS / Fremont DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI143673 United States
CitationJournal: Cell / Year: 2025
Title: Structural basis for plasticity in receptor engagement by an encephalitic alphavirus.
Authors: Saravanan Raju / Sathvik Palakurty / Alan Sariol / Ngan Wagoner / Lucas J Adams / Sean Hui / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit ...The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit different patterns of engagement for two of their entry receptors: very-low-density lipoprotein receptor (VLDLR) and protocadherin 10 (PCDH10). Using structural and functional studies, we show that while all WEEV strains have a lipoprotein class A (LA) domain binding site near the E1 fusion loop, VLDLR engagement requires a second binding site in E2 that can vary with single nucleotide substitutions. We also resolve a structure of PCDH10 bound to WEEV, which reveals interactions near the E1 fusion loop with residues that also mediate LA domain binding. Evolutionary analysis enabled the generation of a PCDH10 decoy that protects in vivo against all WEEV strains tested. Our experiments demonstrate how viruses can engage multiple receptors using shared determinants, which likely impacts cellular tropism and virulence.
History
DepositionNov 11, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47846.png

Downloads & links

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Map

FileDownload / File: emd_47846.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 300 pix.
= 333. Å		1.11 Å/pix.
x 300 pix.
= 333. Å		1.11 Å/pix.
x 300 pix.
= 333. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-3.1248538 - 4.597598
Average (Standard dev.)0.0015010161 (±0.14437094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 333.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47846_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47846_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 : Ross river virus (STRAIN T48)

EntireName: Ross river virus (STRAIN T48)
Components
  • Virus: Ross river virus (STRAIN T48)
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION

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Supramolecule #1: Ross river virus (STRAIN T48)

SupramoleculeName: Ross river virus (STRAIN T48) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 11032 / Sci species name: Ross river virus (STRAIN T48) / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Ross river virus (STRAIN T48)
Molecular weightTheoretical: 47.432598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVVETSLEP TLNLEYITCE YKTVVPSPFI KCCGTSECSS KEQPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCKHDHA SAYKAHTASL KATIRISYGT INQTTEAFVN GEHAVNVGGS K FIFGPIST ...String:
YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVVETSLEP TLNLEYITCE YKTVVPSPFI KCCGTSECSS KEQPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCKHDHA SAYKAHTASL KATIRISYGT INQTTEAFVN GEHAVNVGGS K FIFGPIST AWSPFDNKIV VYKDDVYNQD FPPYGSGQPG RFGDIQSRTV ESKDLYANTA LKLSRPSPGV VHVPYTQTPS GF KYWLKEK GSSLNTKAPF GCKIKTNPVR AMDCAVGSIP VSMDIPDSAF TRVVDAPAVT DLSCQVVVCT HSSDFGGVAT LSY KTDKPG DCAVHSHSNV ATLQEATVKV KTAGKVTVHF STASASPAFK VSVCDAKTTC TAACEPPKDH IVPYGASHNN QVFP DMSGT AMTWVQRLAS GLGGLALIAV VVLVLVTCIT MRR

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: Ross river virus (STRAIN T48)
Molecular weightTheoretical: 46.427855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVTEHFNVYK ATRPYLAYCA DCGDGYFCYS PVAIEKIRDE ASDGMLKIQV SAQIGLDKAG THAHTKIRYM AGHDVQESKR DSLRVYTSA ACSIHGTMGH FIVAHCPPGD YLKVSFEDAD SHVKACKVQY KHDPLPVGRE KFVVRPHFGV ELPCTSYQLT T APTDEEID ...String:
SVTEHFNVYK ATRPYLAYCA DCGDGYFCYS PVAIEKIRDE ASDGMLKIQV SAQIGLDKAG THAHTKIRYM AGHDVQESKR DSLRVYTSA ACSIHGTMGH FIVAHCPPGD YLKVSFEDAD SHVKACKVQY KHDPLPVGRE KFVVRPHFGV ELPCTSYQLT T APTDEEID MHTPPDIPDR TLLSQTAGNV KITAGGRTIR YNCTCGRDNV GTTSTDKTIN TCKIDQCHAA VTSHDKWQFT SP FVPRADQ TARRGKVHVP FPLTNVTCRV PLARAPDVTY GKKEVTLRLH PDHPTLFSYR SLGAEPHPYE EWVDKFSERI IPV TEEGIE YQWGNNPPVR LWAQLTTEGK PHGWPHEIIQ YYYGLYPAAT IAAVSGASLM ALLTLAATCC MLATARRKCL TPYA LTPGA VVPLTLGLLC CAPR

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: Ross river virus (STRAIN T48)
Molecular weightTheoretical: 17.367848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RMCMKIENDC IFEVKLDGKV TGYACLVGDK VMKPAHVKGT IDNPDLAKLT YKKSSKYDLE CAQIPVHMKS DASKYTHEKP EGHYNWHHG AVQYSGGRFT IPTGAGKPGD SGRPIFDNKG RVVAIVLGGA NEGARTALSV VTWTKDMVTR VTPEGTEEW

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.361682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RTCRIHEISC GAHSTQCIPV SWRCDGENDC DSGEDEENC

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / 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: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1173256
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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