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- PDB-8x0l: Cryo-EM structure of Semliki Forest virus in complex with its rec... -

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Basic information

Entry
Database: PDB / ID: 8x0l
TitleCryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Components
  • (pike glycoprotein ...) x 2
  • Capsid protein
  • Very low-density lipoprotein receptor
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


reelin receptor activity / glycoprotein transport / VLDL clearance / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / 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 / glycoprotein transport / VLDL clearance / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / 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 / 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 / host cell nucleus / virion attachment to host cell / host cell plasma membrane / glutamatergic synapse / structural molecule activity / virion membrane / signal transduction / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
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. / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGao, F.G. / Liu, S.
Funding support China, 1items
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, F.G. / Liu, S.
History
DepositionNov 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: pike glycoprotein E2
C: pike glycoprotein E1
E: Capsid protein
F: pike glycoprotein E2
G: pike glycoprotein E1
I: Capsid protein
J: pike glycoprotein E2
K: pike glycoprotein E1
H: Very low-density lipoprotein receptor
D: Very low-density lipoprotein receptor
L: Very low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,95324
Polymers347,62312
Non-polymers3,33012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Pike glycoprotein ... , 2 types, 6 molecules BFJCGK

#2: Protein pike glycoprotein E2


Mass: 46432.777 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A0E3T652
#3: Protein pike glycoprotein E1


Mass: 47489.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A0F6PP03

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Protein / Protein/peptide / Non-polymers , 3 types, 9 molecules AEIHDL

#1: Protein Capsid protein


Mass: 17848.350 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P03315
#4: Protein/peptide Very low-density lipoprotein receptor


Mass: 4103.384 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P98155
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 2 types, 9 molecules

#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Semliki Forest virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 563953 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325185
ELECTRON MICROSCOPYf_angle_d0.64834278
ELECTRON MICROSCOPYf_dihedral_angle_d4.4013498
ELECTRON MICROSCOPYf_chiral_restr0.0453843
ELECTRON MICROSCOPYf_plane_restr0.0064416

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