[English] 日本語
Yorodumi
- PDB-5oyl: VSV G CR2 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / 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 / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / negative regulation of receptor recycling / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / 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 / cellular response to low-density lipoprotein particle stimulus / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / amyloid-beta clearance / sorting endosome / lipoprotein particle binding / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / cholesterol homeostasis / lipid metabolic process / positive regulation of inflammatory response / endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / virus receptor activity / late endosome / apical part of cell / amyloid-beta binding / basolateral plasma membrane / protease binding / receptor complex / molecular adaptor activity / endosome membrane / early endosome / lysosome / 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 / cell surface / Golgi apparatus / identical protein binding / membrane / 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 / Growth factor receptor cysteine-rich domain superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more