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- EMDB-39619: Semliki Forest virus viron in complex with VLDLR -

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Basic information

Entry
Database: EMDB / ID: EMD-39619
TitleSemliki Forest virus viron in complex with VLDLR
Map data
Sample
  • Organelle or cellular component: Semliki Forest virus viron in complex with VLDLR-LA3-5
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Very low-density lipoprotein receptor
    • Protein or peptide: capsid protein, partial
    • Protein or peptide: Spike glycoprotein E3
KeywordsSemliki Forest virus / VLDLR / 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 / very-low-density lipoprotein particle / cargo receptor activity / 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 / receptor complex / lysosomal membrane / calcium ion binding / glutamatergic synapse / signal transduction / 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 / 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 ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
: / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesSemliki Forest virus 4 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWang J / Zheng T / Yang D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Semliki Forest virus at 3.02 Angstroms resolution
Authors: Zheng T
History
DepositionMar 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39619.png

Downloads & links

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Map

FileDownload / File: emd_39619.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: 0.2
Minimum - Maximum-1.6919413 - 2.8291574
Average (Standard dev.)0.0048709367 (±0.12327772)
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: #1

Fileemd_39619_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_39619_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 : Semliki Forest virus viron in complex with VLDLR-LA3-5

EntireName: Semliki Forest virus viron in complex with VLDLR-LA3-5
Components
  • Organelle or cellular component: Semliki Forest virus viron in complex with VLDLR-LA3-5
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Very low-density lipoprotein receptor
    • Protein or peptide: capsid protein, partial
    • Protein or peptide: Spike glycoprotein E3

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Supramolecule #1: Semliki Forest virus viron in complex with VLDLR-LA3-5

SupramoleculeName: Semliki Forest virus viron in complex with VLDLR-LA3-5
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Semliki Forest virus 4

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 47.489766 KDa
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: UNIPROTKB: A0A0E3T652

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Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2
Details: Molecular name is based on https://www.ebi.ac.uk/interpro/protein/UniProt/A0A0E3T652/ as Uniprot Reference A0A0E3T652 and author provided name are both Structural polyprotein.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 46.468867 KDa
SequenceString: HFNVYKATRP YIAYCADCGA GHSCHSPVAI EAVRSEATDG MLKIQFSAQI GIDKSDNHDY TKIRYADGHA IENAVRSSLK VATSGDCFV HGTMGHFILA KCPPGEFLQV SIQDTRNAVR ACRIQYHHDP QPVGREKFTI RPHYGKEIPC TTYQQTTAKT V EEIDMHMP ...String:
HFNVYKATRP YIAYCADCGA GHSCHSPVAI EAVRSEATDG MLKIQFSAQI GIDKSDNHDY TKIRYADGHA IENAVRSSLK VATSGDCFV HGTMGHFILA KCPPGEFLQV SIQDTRNAVR ACRIQYHHDP QPVGREKFTI RPHYGKEIPC TTYQQTTAKT V EEIDMHMP PDTPDRTLLS QQSGNVKITV GGKKVKYNCT CGTGNVGTTN SDMTINTCLI EQCHVSVTDH KKWQFNSPFV PR ADEPARK GKVHIPFPLD NITCRVPMAR EPTVIHGKRE VTLHLHPDHP TLFSYRTLGE DPQYHEEWVT AAVERTIPVP VDG MEYHWG NNDPVRLWSQ LTTEGKPHGW PHQIVQYYYG LYPAATVSAV VGMSLLALIS IFASCYMLVA ARSKCLTPYA LTPG AAVPW TLGILCCAPR AHA

UniProtKB: UNIPROTKB: A0A0E3T652

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.075933 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RTCRIHEISC GAHSTQCIPV SWRCDGENDC DSGEDEENCG NITCSPDEFT CSSGRCISRN FVCNGQDDCS DGSDELDCAP PTCGAHEFQ CSTSSCIPIS WVCDDDADCS DQSDESLEQC GR

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #4: capsid protein, partial

MacromoleculeName: capsid protein, partial / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 17.791299 KDa
SequenceString:
KRERMCMKIE NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGVIDNADLA KLAFKKSSKY DLECAQIPVH MRSDASKYTH EKPEGHYNW HHGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGSRTA LSVVTWNKDM VTRVTPEGSE E W

UniProtKB: UNIPROTKB: A0A0E3T652

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Macromolecule #5: Spike glycoprotein E3

MacromoleculeName: Spike glycoprotein E3 / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 5.848729 KDa
SequenceString:
MCVLANATFP CFQPPCVPCC YENNAEATLR MLEDNVDRPG YYDLLQAALT CR

UniProtKB: UNIPROTKB: A0A0E3T652

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 3.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44701
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8yw1:
Semliki Forest virus viron in complex with VLDLR

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