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- EMDB-35451: Structure of Semliki Forest virus VLP in complex with the recepto... -

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Basic information

Entry
Database: EMDB / ID: EMD-35451
TitleStructure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3
Map data
Sample
  • Complex: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle / togavirin / positive regulation of dendrite development / dendrite morphogenesis / T=4 icosahedral viral capsid / cargo receptor activity / virion assembly / lipid transport / small molecule binding / apolipoprotein binding / clathrin-coated pit / cholesterol metabolic process / 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 / receptor complex / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / calcium ion binding / virion attachment to host cell / host cell plasma membrane / 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 / Alphavirus E2 glycoprotein, domain A ...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. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Epidermal growth factor-like 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 / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesSemliki Forest virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsCao D / Ma B / Cao Z / Zhang X / Xiang Y
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Cell / Year: 2023
Title: Structure of Semliki Forest virus in complex with its receptor VLDLR.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xinzheng Zhang / Ye Xiang /
Abstract: Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used ...Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used cryoelectron microscopy to study the structure of SFV in complex with VLDLR. We found that VLDLR binds multiple E1-DIII sites of SFV through its membrane-distal LDLR class A (LA) repeats. Among the LA repeats of the VLDLR, LA3 has the best binding affinity to SFV. The high-resolution structure shows that LA3 binds SFV E1-DIII through a small surface area of 378 Å, with the main interactions at the interface involving salt bridges. Compared with the binding of single LA3s, consecutive LA repeats around LA3 promote synergistic binding to SFV, during which the LAs undergo a rotation, allowing simultaneous key interactions at multiple E1-DIII sites on the virion and enabling the binding of VLDLRs from divergent host species to SFV.
History
DepositionFeb 23, 2023-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35451.png

Downloads & links

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Map

FileDownload / File: emd_35451.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.08397801 - 0.1398375
Average (Standard dev.)0.00047634874 (±0.0059196614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35451_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35451_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_35451_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 VLP in complex with its receptor VLDLR at th...

EntireName: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
Components
  • Complex: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Semliki Forest virus VLP in complex with its receptor VLDLR at th...

SupramoleculeName: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Semliki Forest virus

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Macromolecule #1: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 46.870277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AKTVEEID ...String:
SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AKTVEEID MHMPPDTPDR TLLSQQSGNV KITVGGKKVK YNCTCGTGNV GTTNSDMTIN TCLIEQCHVS VTDHKKWQFN SP FVPRADE PARKGKVHIP FPLDNITCRV PMAREPTVIH GKREVTLHLH PDHPTLFSYR TLGEDPQYHE EWVTAAVERT IPV PVDGME YHWGNNDPVR LWSQLTTEGK PHGWPHQIVQ YYYGLYPAAT VSAVVGMSLL ALISIFASCY MLVAARSKCL TPYA LTPGA AVPWTLGILC CAPRAHA

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Macromolecule #2: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 2 / 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

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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: Semliki Forest virus
Molecular weightTheoretical: 17.84835 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GKRERMCMKI ENDCIFEVKH EGKVTGYACL VGDKVMKPAH VKGVIDNADL AKLAFKKSSK YDLECAQIPV HMRSDASKYT HEKPEGHYN WHHGAVQYSG GRFTIPTGAG KPGDSGRPIF DNKGRVVAIV LGGANEGSRT ALSVVTWNKD MVTRVTPEGS E EW

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

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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: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 3 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 651086

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