[English] 日本語
Yorodumi
- PDB-1odq: PEPTIDE OF HUMAN APOA-I RESIDUES 166-185. NMR, 5 STRUCTURES AT PH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1odq
TitlePEPTIDE OF HUMAN APOA-I RESIDUES 166-185. NMR, 5 STRUCTURES AT PH 3.7, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:40
ComponentsAPOA-I PEPTIDE
KeywordsLIPID TRANSPORT / APOLIPOPROTEIN A-I / COFACTOR FOR LCAT ACTIVATION
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / cholesterol import / blood vessel endothelial cell migration / high-density lipoprotein particle binding / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of cholesterol metabolic process / cellular response to lipoprotein particle stimulus / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / high-density lipoprotein particle remodeling / phospholipid homeostasis / reverse cholesterol transport / chemorepellent activity / high-density lipoprotein particle assembly / lipid storage / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / endothelial cell proliferation / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / adrenal gland development / negative chemotaxis / cholesterol binding / cholesterol biosynthetic process / positive regulation of Rho protein signal transduction / amyloid-beta formation / endocytic vesicle / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / positive regulation of phagocytosis / positive regulation of stress fiber assembly / heat shock protein binding / positive regulation of substrate adhesion-dependent cell spreading / endocytic vesicle lumen / cholesterol metabolic process / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular vesicle / amyloid-beta binding / cytoplasmic vesicle / : / secretory granule lumen / blood microparticle / early endosome / protein stabilization / G protein-coupled receptor signaling pathway / receptor ligand activity / Amyloid fiber formation / endoplasmic reticulum lumen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsWang, G. / Treleaven, W.D. / Cushley, R.J.
CitationJournal: Biochim.Biophys.Acta / Year: 1996
Title: Conformation of human serum apolipoprotein A-I(166-185) in the presence of sodium dodecyl sulfate or dodecylphosphocholine by 1H-NMR and CD. Evidence for specific peptide-SDS interactions.
Authors: Wang, G. / Treleaven, W.D. / Cushley, R.J.
History
DepositionMar 2, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APOA-I PEPTIDE


Theoretical massNumber of molelcules
Total (without water)2,3371
Polymers2,3371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 20MOST CLOSELY RESEMBLING THE AVERAGE STRUCTURE OF OF A CALCULATED SET OF 20 CONFORMERS
Representative

-
Components

#1: Protein/peptide APOA-I PEPTIDE / APOA-I (166 - 185) / APOLIPOPROTEIN A-I (166 - 185)


Mass: 2336.605 Da / Num. of mol.: 1 / Fragment: RESIDUES 166 - 185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02647

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 3.7 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR software
NameDeveloperClassification
DGIIHAVELrefinement
DiscoverBIOSYM TECHNOLOGIES, INC.refinement
NMR ensembleConformer selection criteria: MOST CLOSELY RESEMBLING THE AVERAGE STRUCTURE OF OF A CALCULATED SET OF 20 CONFORMERS
Conformers calculated total number: 20 / Conformers submitted total number: 5

+
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