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- PDB-5oy9: VSV G CR3 -

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Basic information

Entry
Database: PDB / ID: 5oy9
TitleVSV G CR3
Components
  • Glycoprotein G
  • Low-density lipoprotein receptor
KeywordsVIRAL PROTEIN / c
Function / homology
Function and homology information


regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling ...regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / intestinal cholesterol absorption / low-density lipoprotein particle binding / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / amyloid-beta clearance / sorting endosome / lipoprotein particle binding / 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 / clathrin-dependent endocytosis of virus by host cell / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / fusion of virus membrane with host endosome membrane / viral envelope / calcium ion binding / positive regulation of gene expression / virion attachment to host cell / virion membrane / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane
Similarity search - Function
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. ...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
Similarity search - Domain/homology
Low-density lipoprotein receptor / Glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Vesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 8, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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 G
D: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0388
Polymers50,2322
Non-polymers8066
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-11 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.350, 122.350, 197.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-504-

CA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein Glycoprotein G


Mass: 46097.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Vesicular stomatitis Indiana virus (strain Mudd-Summers)
Strain: Mudd-Summers / References: UniProt: P0C2X0
#2: Protein/peptide Low-density lipoprotein receptor / LDL receptor


Mass: 4134.462 Da / Num. of mol.: 1 / Fragment: UNP residues 108-144
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

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Sugars , 2 types, 2 molecules

#3: 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.: 1 / Source method: obtained synthetically
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
#4: 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.: 1 / 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 , 2 types, 7 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.8 Å3/Da / Density % sol: 74.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 400, 50 mM Tris-HCl pH 8.5, 200 mM CaCl2, 0.2% dodecylmaltoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.6→46.7 Å / Num. obs: 10749 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 148.6 Å2 / Rmerge(I) obs: 0.286 / Net I/σ(I): 9.75
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 13.6 % / Rmerge(I) obs: 5.305 / Mean I/σ(I) obs: 0.7 / Rpim(I) all: 1.443 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6J

2j6j
PDB Unreleased entry


Resolution: 3.6→44.85 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.268 537 5.01 %
Rwork0.236 --
obs0.237 10727 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 156.7 Å2
Refinement stepCycle: LAST / Resolution: 3.6→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 46 3 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063694
X-RAY DIFFRACTIONf_angle_d0.8195035
X-RAY DIFFRACTIONf_dihedral_angle_d15.332179
X-RAY DIFFRACTIONf_chiral_restr0.05538
X-RAY DIFFRACTIONf_plane_restr0.005644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6002-3.96240.30621300.30292458X-RAY DIFFRACTION100
3.9624-4.53520.2651310.22062487X-RAY DIFFRACTION100
4.5352-5.71210.24811330.21972528X-RAY DIFFRACTION100
5.7121-44.84970.27051430.23522717X-RAY DIFFRACTION100

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