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- EMDB-37981: Cryo-EM structure of Semliki Forest virus in complex with its rec... -

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Entry
Database: EMDB / ID: EMD-37981
TitleCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Map dataCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Sample
  • Complex: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
    • Protein or peptide: Capsid protein
    • Protein or peptide: pike glycoprotein E2
    • Protein or peptide: pike glycoprotein E1
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsVIRAL 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 / virion assembly / small molecule binding / apolipoprotein binding / clathrin-coated pit / receptor-mediated endocytosis / cholesterol metabolic process / 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 / symbiont entry into host cell / viral translational frameshifting / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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
Similarity search - Component
Biological speciesSemliki Forest virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGao FG / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)
Authors: Gao FG / Liu S
History
DepositionNov 4, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37981.png

Downloads & links

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Map

FileDownload / File: emd_37981.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017511563 - 2.014662
Average (Standard dev.)0.007445162 (±0.062537394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of Semliki Forest virus in complex...

Fileemd_37981_half_map_1.map
AnnotationCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Semliki Forest virus in complex...

Fileemd_37981_half_map_2.map
AnnotationCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Semliki Forest virus in complex with its rec...

EntireName: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Components
  • Complex: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
    • Protein or peptide: Capsid protein
    • Protein or peptide: pike glycoprotein E2
    • Protein or peptide: pike glycoprotein E1
    • 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: Cryo-EM structure of Semliki Forest virus in complex with its rec...

SupramoleculeName: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Semliki Forest virus

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
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

UniProtKB: Structural polyprotein

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Macromolecule #2: pike glycoprotein E2

MacromoleculeName: pike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 46.432777 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 CAP

UniProtKB: UNIPROTKB: A0A0E3T652

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Macromolecule #3: pike glycoprotein E1

MacromoleculeName: pike glycoprotein E1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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 #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: 4.103384 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CRIHEISCGA HSTQCIPVSW RCDGENDCDS GEDEENC

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 563953
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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