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- PDB-5oyl: VSV G CR2 -

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Basic information

Entry
Database: PDB / ID: 5oyl
TitleVSV G CR2
Components
  • Glycoprotein
  • Low-density lipoprotein receptor
KeywordsVIRAL PROTEIN / c
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / PCSK9-LDLR complex / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of receptor recycling / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / negative regulation of low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / PCSK9-LDLR complex / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of receptor recycling / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / negative regulation of low-density lipoprotein particle clearance / cholesterol import / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle binding / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / low-density lipoprotein particle receptor activity / LDL clearance / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / endolysosome membrane / cholesterol transport / low-density lipoprotein particle / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / sorting endosome / lipoprotein particle binding / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / symbiont entry into host cell / external side of plasma membrane / negative regulation of gene expression / viral envelope / calcium ion binding / positive regulation of gene expression / virion attachment to host cell / Golgi apparatus / cell surface / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Rhabdovirus glycoprotein / Rhabdovirus spike 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 / Low-density lipoprotein receptor domain class A ...Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Rhabdovirus glycoprotein / Rhabdovirus spike 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 / 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. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Glycoprotein / Low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAlbertini, A.A. / Belot, L. / Legrand, P. / Gaudin, Y.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0020 France
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein.
Authors: Nikolic, J. / Belot, L. / Raux, H. / Legrand, P. / Gaudin, Y. / A Albertini, A.
History
DepositionSep 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein
D: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,34014
Polymers50,9512
Non-polymers1,38812
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-20 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.040, 90.040, 515.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-719-

HOH

31A-726-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules AD

#1: Protein Glycoprotein


Mass: 46097.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
References: UniProt: B7UCZ5
#2: Protein/peptide Low-density lipoprotein receptor / LDL receptor


Mass: 4853.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Escherichia coli (E. coli) / References: UniProt: P01130
#3: 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
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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Non-polymers , 3 types, 158 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 29% PEG 3000, 100 mM Tris-HCl pH 8.5, 200 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.24→49.68 Å / Num. obs: 39498 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.061 / Rrim(I) all: 0.203 / Net I/σ(I): 8.7
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2829 / CC1/2: 0.494 / Rpim(I) all: 1.741 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I2S

5i2s


Resolution: 2.25→29.979 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2238 1493 5 %
Rwork0.1882 --
obs0.1899 29832 76.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.33 Å2 / Biso mean: 59.5437 Å2 / Biso min: 21.93 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 86 149 3812

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