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- PDB-8yw2: Semliki Forest virus viron in complex with VLDLR -

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Basic information

Entry
Database: PDB / ID: 8yw2
TitleSemliki Forest virus viron in complex with VLDLR
Components
  • (Spike glycoprotein ...) x 3
  • Very low-density lipoprotein receptor
  • capsid protein, partial
KeywordsVIRAL PROTEIN / Semliki Forest virus viron / VLDLR
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 speciesHomo sapiens (human)
Semliki Forest virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, J. / Zheng, T. / Yang, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Semliki Forest virus in complex with VLDLR
Authors: Zheng, T.
History
DepositionMar 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Spike glycoprotein E3
1: capsid protein, partial
2: Spike glycoprotein E3
3: capsid protein, partial
4: Spike glycoprotein E1
5: Spike glycoprotein E1
6: Spike glycoprotein E1
7: Spike glycoprotein E2
8: Spike glycoprotein E2
9: Spike glycoprotein E2
A: Very low-density lipoprotein receptor
AA: Spike glycoprotein E3
AB: Spike glycoprotein E3
AC: capsid protein, partial
AD: capsid protein, partial
AE: capsid protein, partial
B: Spike glycoprotein E2
D: capsid protein, partial
E: Spike glycoprotein E1
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E2
J: Spike glycoprotein E2
K: Spike glycoprotein E2
L: Spike glycoprotein E3
M: Spike glycoprotein E3
N: Spike glycoprotein E3
O: capsid protein, partial
P: capsid protein, partial
Q: capsid protein, partial
R: Spike glycoprotein E2
S: Spike glycoprotein E3
T: capsid protein, partial
U: Spike glycoprotein E1
V: Spike glycoprotein E1
W: Spike glycoprotein E1
X: Spike glycoprotein E2
Y: Spike glycoprotein E2
Z: Spike glycoprotein E2
a: Spike glycoprotein E3
b: Spike glycoprotein E3
c: Spike glycoprotein E3
d: capsid protein, partial
e: capsid protein, partial
f: capsid protein, partial
g: Spike glycoprotein E3
h: Spike glycoprotein E1
i: Spike glycoprotein E1
j: Spike glycoprotein E2
l: Spike glycoprotein E3
m: Spike glycoprotein E1
n: capsid protein, partial
o: Spike glycoprotein E1
p: Spike glycoprotein E1
q: Spike glycoprotein E1
r: Spike glycoprotein E2
s: Spike glycoprotein E2
t: Spike glycoprotein E2
u: Spike glycoprotein E3
v: Spike glycoprotein E3
w: Spike glycoprotein E3
x: capsid protein, partial
y: capsid protein, partial
z: Spike glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,927,318113
Polymers1,899,16465
Non-polymers28,15448
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Spike glycoprotein ... , 3 types, 48 molecules 02AAABLMNSabcgluvw456EFGHUVWhimo...

#1: Protein
Spike glycoprotein E3 / p130


Mass: 5848.729 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#3: Protein
Spike glycoprotein E1 / p130


Mass: 47489.766 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#4: Protein
Spike glycoprotein E2 / p130


Mass: 46468.867 Da / Num. of mol.: 16 / Source method: isolated from a natural source
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.
Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652

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Protein , 2 types, 17 molecules 13ACADAEDOPQTdefnxyA

#2: Protein
capsid protein, partial / p130


Mass: 17791.299 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#5: Protein Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 17585.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155

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Sugars , 1 types, 48 molecules

#6: Polysaccharide...
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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: Semliki Forest viron / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Semliki Forest virus 41642950
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33471 / Symmetry type: POINT

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