[English] 日本語
Yorodumi
- PDB-1ya9: Crystal Structure of the 22kDa N-Terminal Fragment of Mouse Apoli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ya9
TitleCrystal Structure of the 22kDa N-Terminal Fragment of Mouse Apolipoprotein E
ComponentsApolipoprotein E
KeywordsLIPID TRANSPORT / Apolipoprotein E / LDL receptor binding
Function / homology
Function and homology information


maintenance of location in cell / negative regulation of postsynaptic membrane organization / negative regulation of phospholipid efflux / negative regulation of lipid transport across blood-brain barrier / Chylomicron clearance / positive regulation of neurofibrillary tangle assembly / negative regulation of triglyceride metabolic process / positive regulation of presynaptic membrane organization / Chylomicron assembly / Chylomicron remodeling ...maintenance of location in cell / negative regulation of postsynaptic membrane organization / negative regulation of phospholipid efflux / negative regulation of lipid transport across blood-brain barrier / Chylomicron clearance / positive regulation of neurofibrillary tangle assembly / negative regulation of triglyceride metabolic process / positive regulation of presynaptic membrane organization / Chylomicron assembly / Chylomicron remodeling / HDL remodeling / regulation of plasma lipoprotein particle levels / Scavenging by Class A Receptors / regulation of triglyceride metabolic process / lipoprotein catabolic process / hydroxyapatite binding / Retinoid metabolism and transport / extrinsic component of external side of plasma membrane / negative regulation of lipid biosynthetic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of cholesterol efflux / negative regulation of dendritic spine development / lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / chylomicron remnant clearance / chylomicron remnant / lipoprotein particle / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / artery development / circulatory system development / intermediate-density lipoprotein particle / NMDA glutamate receptor clustering / cholesterol catabolic process / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipoprotein metabolic process / positive regulation of low-density lipoprotein particle receptor catabolic process / very-low-density lipoprotein particle clearance / cellular response to lipoprotein particle stimulus / lipoprotein biosynthetic process / response to caloric restriction / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / high-density lipoprotein particle remodeling / positive regulation of amyloid-beta clearance / triglyceride metabolic process / reverse cholesterol transport / very-low-density lipoprotein particle / regulation of amyloid fibril formation / positive regulation of cholesterol metabolic process / high-density lipoprotein particle assembly / low-density lipoprotein particle / host-mediated activation of viral process / multivesicular body, internal vesicle / melanosome organization / high-density lipoprotein particle / cholesterol transfer activity / artery morphogenesis / blood vessel development / amyloid precursor protein metabolic process / protein import / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / lipid transport / negative regulation of protein metabolic process / regulation of behavioral fear response / heparan sulfate proteoglycan binding / negative regulation of endothelial cell migration / positive regulation of membrane protein ectodomain proteolysis / regulation of Cdc42 protein signal transduction / regulation of amyloid precursor protein catabolic process / cholesterol efflux / regulation of cholesterol metabolic process / negative regulation of dendritic spine maintenance / response to dietary excess / triglyceride homeostasis / low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta formation / virion assembly / regulation of innate immune response / positive regulation of dendritic spine development / negative regulation of endothelial cell proliferation / antioxidant activity / lipid carrier activity / positive regulation of lipoprotein transport / negative regulation of platelet-derived growth factor receptor signaling pathway / regulation of synapse organization / locomotory exploration behavior
Similarity search - Function
Apolipoprotein / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPeters-Libeu, C.A. / Rutenber, E. / Newhouse, Y. / Hatters, D.M. / Weisgraber, K.H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Engineering conformational destabilization into mouse apolipoprotein E. A model for a unique property of human apolipoprotein E4
Authors: Hatters, D.M. / Peters-Libeu, C.A. / Weisgraber, K.H.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apolipoprotein E


Theoretical massNumber of molelcules
Total (without water)21,0531
Polymers21,0531
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.034, 49.233, 112.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 21052.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoe / Production host: Escherichia coli (E. coli)
Keywords: 22kDa N-Terminal Fragment of Mouse Apolipoprotein E, (residue 20-200, SWS)
References: UniProt: P08226
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.9 Å3/Da / Density % sol: 35.4 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.09→20 Å / Num. all: 10097 / Num. obs: 9944 / Biso Wilson estimate: 14.1 Å2
Reflection shellResolution: 2.09→2.13 Å / % possible all: 87

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
EPMRphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→18.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0.01 / SU B: 6.261 / SU ML: 0.171 / Data cutoff high absF: 1263371.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 512 5.1 %RANDOM
Rwork0.215 ---
obs0.215 9944 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1753 Å2 / ksol: 0.352492 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---2.75 Å20 Å2
3---4.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.09→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 83 1448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.09→2.13 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 20 4.9 %
Rwork0.229 391 -
obs--22 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

+
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://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