[English] 日本語
Yorodumi
- PDB-1or3: APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1or3
TitleAPOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165
ComponentsPROTEIN (APOLIPOPROTEIN E)
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA PROTEIN / HDL / VLDL
Function / homology
Function and homology information


positive regulation of heparan sulfate proteoglycan binding / lipid transport involved in lipid storage / chylomicron remnant / 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 / positive regulation of low-density lipoprotein particle receptor catabolic process / metal chelating activity / triglyceride-rich lipoprotein particle clearance / lipoprotein particle ...positive regulation of heparan sulfate proteoglycan binding / lipid transport involved in lipid storage / chylomicron remnant / 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 / positive regulation of low-density lipoprotein particle receptor catabolic process / metal chelating activity / triglyceride-rich lipoprotein particle clearance / lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / regulation of amyloid-beta clearance / negative regulation of cholesterol biosynthetic process / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / very-low-density lipoprotein particle clearance / Chylomicron clearance / NMDA glutamate receptor clustering / acylglycerol homeostasis / response to caloric restriction / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / negative regulation of triglyceride metabolic process / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / regulation of amyloid fibril formation / regulation of behavioral fear response / regulation of protein metabolic process / high-density lipoprotein particle clearance / chylomicron / lipoprotein catabolic process / lipid transporter activity / high-density lipoprotein particle remodeling / phospholipid efflux / melanosome organization / multivesicular body, internal vesicle / AMPA glutamate receptor clustering / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / positive regulation of amyloid-beta clearance / very-low-density lipoprotein particle / positive regulation by host of viral process / low-density lipoprotein particle / lipoprotein biosynthetic process / positive regulation of CoA-transferase activity / protein import / high-density lipoprotein particle / negative regulation of blood coagulation / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / regulation of amyloid precursor protein catabolic process / cholesterol catabolic process / triglyceride homeostasis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of protein metabolic process / HDL remodeling / triglyceride metabolic process / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / cholesterol efflux / low-density lipoprotein particle receptor binding / artery morphogenesis / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / virion assembly / positive regulation of dendritic spine development / regulation of innate immune response / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / regulation of neuronal synaptic plasticity / antioxidant activity / lipoprotein particle binding / positive regulation of endocytosis / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / positive regulation of cholesterol efflux / regulation of protein-containing complex assembly / intracellular transport / fatty acid homeostasis / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / regulation of proteasomal protein catabolic process
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.73 Å
AuthorsRupp, B. / Segelke, B.W.
CitationJournal: Protein Sci. / Year: 2000
Title: Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding.
Authors: Segelke, B.W. / Forstner, M. / Knapp, M. / Trakhanov, S.D. / Parkin, S. / Newhouse, Y.M. / Bellamy, H.D. / Weisgraber, K.H. / Rupp, B.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (APOLIPOPROTEIN E)


Theoretical massNumber of molelcules
Total (without water)19,2981
Polymers19,2981
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.370, 47.370, 104.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-114-

ARG

21A-212-

HOH

-
Components

#1: Protein PROTEIN (APOLIPOPROTEIN E) / APOE3


Mass: 19297.805 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE MUTANT USED IN MAD PHASING EXPERIMENT
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21, B834(DE)MET- / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, B834(DE)MET- / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.76 Å3/Da / Density % sol: 30 %
Description: 4 WAVELENGTHS USED FOR PHASING (ALS BEAMLINE 5.0.2)
Crystal growpH: 5.6
Details: RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2).
Components of the solutions
IDNameCrystal-IDSol-ID
150MM NA-Cacodylate, pH 5.612
210-20% PEG 40012
31% 2-ME12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 %PEG4001reservoir
250 mMsodium cacodylate1reservoir
320 mM1dropNH4HCO3
45 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: May 15, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→25 Å / Num. obs: 16782 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 27.4
Reflection shellResolution: 1.73→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.7 / Rsym value: 22.5 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 48854
Reflection shell
*PLUS
% possible obs: 89.9 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
X-PLORmodel building
CCP4model building
X-PLOR3.851refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.73→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1339 10.1 %RANDOM
Rwork0.229 ---
obs-13222 89.9 %-
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-3.35 Å20 Å2
2---1.23 Å20 Å2
3---2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-8 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.73→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 158 1306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.291.5
X-RAY DIFFRACTIONx_mcangle_it6.622
X-RAY DIFFRACTIONx_scbond_it7.232
X-RAY DIFFRACTIONx_scangle_it11.12.5
LS refinement shellResolution: 1.73→1.79 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 967 10.4 %
Rwork0.33 112 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PATOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETE
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.33

+
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