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- EMDB-42054: Structure of Semliki Forest virus VLP in complex with VLDLR LA2 -

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Basic information

Entry
Database: EMDB / ID: EMD-42054
TitleStructure of Semliki Forest virus VLP in complex with VLDLR LA2
Map data
Sample
  • Virus: Semliki Forest virus
    • Protein or peptide: Glycoprotein E1
    • Protein or peptide: Glycoprotein E2
    • Protein or peptide: Assembly protein E3
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsSemliki Forest Virus / Receptor / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / 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 / togavirin ...reelin receptor activity / VLDL clearance / glycoprotein transport / 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 / togavirin / reelin-mediated signaling pathway / very-low-density lipoprotein particle / positive regulation of dendrite development / cargo receptor activity / T=4 icosahedral viral capsid / lipid transport / dendrite morphogenesis / virion assembly / regulation of synapse assembly / small molecule binding / apolipoprotein binding / cholesterol metabolic process / clathrin-coated pit / receptor-mediated endocytosis / VLDLR internalisation and degradation / memory / calcium-dependent protein binding / nervous system development / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / receptor complex / viral translational frameshifting / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / calcium ion binding / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / glutamatergic synapse / virion membrane / 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 / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / 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
Similarity search - Component
Biological speciesSemliki Forest virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAbraham J / Yang P / Li W / Fan X / Pan J
Funding support United States, 1 items
OrganizationGrant numberCountry
Burroughs Wellcome Fund United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus.
Authors: Pan Yang / Wanyu Li / Xiaoyi Fan / Junhua Pan / Colin J Mann / Haley Varnum / Lars E Clark / Sarah A Clark / Adrian Coscia / Himanish Basu / Katherine Nabel Smith / Vesna Brusic / Jonathan Abraham /
Abstract: Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. ...Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.
History
DepositionSep 20, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42054.png

Downloads & links

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Map

FileDownload / File: emd_42054.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 430 pix.
= 354.75 Å		0.83 Å/pix.
x 430 pix.
= 354.75 Å		0.83 Å/pix.
x 430 pix.
= 354.75 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0019632215 - 1.7935587
Average (Standard dev.)0.013247955 (±0.079707064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 354.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_42054_additional_1.map
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Half map: #2

Fileemd_42054_half_map_1.map
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Half map: #1

Fileemd_42054_half_map_2.map
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Sample components

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Entire : Semliki Forest virus

EntireName: Semliki Forest virus
Components
  • Virus: Semliki Forest virus
    • Protein or peptide: Glycoprotein E1
    • Protein or peptide: Glycoprotein E2
    • Protein or peptide: Assembly protein E3
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Semliki Forest virus

SupramoleculeName: Semliki Forest virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 11033 / Sci species name: Semliki Forest virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Glycoprotein E1

MacromoleculeName: Glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 47.489766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTDKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYAASHSN VVFP DMSGT ALSWVQKISG GLGAFAIGAI LVLVVVTCIG LRR

UniProtKB: Structural polyprotein

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Macromolecule #2: Glycoprotein E2

MacromoleculeName: Glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 46.330719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNVYKATRPY IAYCADCGAG HSCHSPVAIE AVRSEATDGM LKIQFSAQIG IDKSDNHDYT KIRYADGHAI ENAVRSSLKV ATSGDCFVH GTMGHFILAK CPPGEFLQVS IQDTRNAVRA CRIQYHHDPQ PVGREKFTIR PHYGKEIPCT TYQQTTAKTV E EIDMHMPP ...String:
FNVYKATRPY IAYCADCGAG HSCHSPVAIE AVRSEATDGM LKIQFSAQIG IDKSDNHDYT KIRYADGHAI ENAVRSSLKV ATSGDCFVH GTMGHFILAK CPPGEFLQVS IQDTRNAVRA CRIQYHHDPQ PVGREKFTIR PHYGKEIPCT TYQQTTAKTV E EIDMHMPP DTPDRTLLSQ QSGNVKITVG GKKVKYNCTC GTGNVGTTNS DMTINTCLIE QCHVSVTDHK KWQFNSPFVP RA DEPARKG KVHIPFPLDN ITCRVPMARE PTVIHGKREV TLHLHPDHPT LFSYRTLGED PQYHEEWVTA AVERTIPVPV DGM EYHWGN NDPVRLWSQL TTEGKPHGWP HQIVQYYYGL YPAATVSAVV GMSLLALISI FASCYMLVAA RSKCLTPYAL TPGA AVPWT LGILCCAPRA HA

UniProtKB: UNIPROTKB: A0A0E3T652

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Macromolecule #3: Assembly protein E3

MacromoleculeName: Assembly protein E3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 6.020911 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TAMCVLANAT FPCFQPPCVP CCYENNAEAT LRMLEDNVDR PGYYDLLQAA LTCR

UniProtKB: Structural polyprotein

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Macromolecule #4: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 16.723904 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IENDCIFEVK HEGKVTGYAC LVGDKVMKPA HVKGVIDNAD LAKLAFKKSS KYDLECAQIP VHMRSDASKY THEKPEGHYN WHHGAVQYS GGRFTIPTGA GKPGDSGRPI FDNKGRVVAI VLGGANEGSR TALSVVTWNK DMVTRVTPEG SEEW

UniProtKB: Structural polyprotein

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Macromolecule #5: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.028225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CAESDFVCNN GQCVPSRWKC DGDPDCEDGS DESPEQC

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 1 / 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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

1015

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 439486
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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