[English] 日本語
Yorodumi
- PDB-1le2: STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1le2
TitleSTRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E
ComponentsAPOLIPOPROTEIN E2
KeywordsLIPOPROTEIN
Function / homology
Function and homology information


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 / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process ...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 / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / positive regulation of lipoprotein transport / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / Chylomicron remodeling / lipid transporter activity / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of amyloid fibril formation / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / regulation of protein metabolic process / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / AMPA glutamate receptor clustering / lipoprotein catabolic process / melanosome organization / multivesicular body, internal vesicle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / Scavenging by Class A Receptors / triglyceride metabolic process / positive regulation of dendritic spine development / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / negative regulation of blood vessel endothelial cell migration / regulation of neuronal synaptic plasticity / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of dendritic spine maintenance / negative regulation of blood coagulation / positive regulation of cholesterol efflux / negative regulation of MAP kinase activity / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport
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 / Resolution: 3 Å
AuthorsWilson, C. / Agard, D.A.
Citation
Journal: Structure / Year: 1994
Title: Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein.
Authors: Wilson, C. / Mau, T. / Weisgraber, K.H. / Wardell, M.R. / Mahley, R.W. / Agard, D.A.
#1: Journal: Science / Year: 1991
Title: Three-Dimensional Structure of the Ldl Receptor-Binding Domain of Human Apolipoprotein E
Authors: Wilson, C. / Wardell, M.R. / Weisgraber, K.H. / Mahley, R.W. / Agard, D.A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Diffraction Studies on the Amino-Terminal (Receptor-Binding) Domain of Human Apolipoprotein E3 from Serum Very Low Density Lipoproteins
Authors: Aggerbeck, L.P. / Wetterau, J.R. / Weisgraber, K.H. / Mahley, R.W. / Agard, D.A.
History
DepositionAug 22, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APOLIPOPROTEIN E2


Theoretical massNumber of molelcules
Total (without water)16,6891
Polymers16,6891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.060, 53.940, 83.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein APOLIPOPROTEIN E2


Mass: 16689.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2 / Production host: unidentified (others) / References: UniProt: P02649
Compound detailsTHREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE APO-E2 ISOFORM DIFFERS FROM THE WILD-TYPE (E3) ...THREE ISOFORMS OF APO-E ARE RELATIVELY COMMON. THE APO-E2 ISOFORM DIFFERS FROM THE WILD-TYPE (E3) PROTEIN BY THE MUTATION ARG158-->CYS. THE MUTANT PROTEIN SHOWS NORMAL LIPOPROTEIN BINDING BUT LESS THAN 2% OF NORMAL LDL RECEPTOR BINDING. THE STRUCTURE OF THE E2 MUTANT WAS DETERMINED USING STARTING PHASES OBTAINED FOR THE E3 PROTEIN. SECONDARY STRUCTURE WAS ASSIGNED USING THE *DEFINE* PROGRAM (RICHARDS AND KUNDROT, PROTEINS V. 3, 71 (1988)).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
215 %PEG4001reservior
320 mMsodium acetate1reservoir
40.2 %beta-n-octylglucopyranoide1reservoir
50.1 %beta-mercaptoethanol1reservoir
1protein1drop

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 2749 / % possible obs: 67.9 %

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.195 / Highest resolution: 3 Å
Details: THE LOOP CONNECTING THE SECOND AND THIRD HELICES OF THE FOUR-HELIX BUNDLE (RESIDUES 83-88) IS POORLY DEFINED IN THE ELECTRON DENSITY MAP. X-PLOR-REFINED COORDINATES FOR THE LOOP HAVE BEEN ...Details: THE LOOP CONNECTING THE SECOND AND THIRD HELICES OF THE FOUR-HELIX BUNDLE (RESIDUES 83-88) IS POORLY DEFINED IN THE ELECTRON DENSITY MAP. X-PLOR-REFINED COORDINATES FOR THE LOOP HAVE BEEN INCLUDED IN THE STRUCTURE BUT ARE LIKELY TO CONTAIN ERRORS.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 0 0 1167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 2749 / σ(I): 2 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.7

+
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