[English] 日本語
Yorodumi
- PDB-3k2s: Solution structure of double super helix model -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k2s
TitleSolution structure of double super helix model
ComponentsApolipoprotein A-I
KeywordsLIPID BINDING PROTEIN / super double helix / amphipathic / Amyloid / Amyloidosis / Atherosclerosis / Cholesterol metabolism / Disease mutation / Glycation / Glycoprotein / HDL / Lipid metabolism / Lipid transport / Lipoprotein / Neuropathy / Palmitate / Secreted / Steroid metabolism / Transport / HIGH DENSITY LIPOPROTEIN
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / 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 / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / high-density lipoprotein particle binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / reverse cholesterol transport / lipid storage / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / 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 / endothelial cell proliferation / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / triglyceride homeostasis / adrenal gland development / negative regulation of interleukin-1 beta production / negative chemotaxis / cholesterol binding / cholesterol biosynthetic process / amyloid-beta formation / positive regulation of Rho protein signal transduction / endocytic vesicle / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / cholesterol metabolic process / Retinoid metabolism and transport / positive regulation of stress fiber assembly / heat shock protein binding / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
CHOLESTEROL / Chem-POV / Apolipoprotein A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / NUCLEAR REACTOR
AuthorsWu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.-M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. ...Wu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.-M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. / Gutsche, I. / Zaccai, G. / Didonato, J.A. / Hazen, L.S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Double superhelix model of high density lipoprotein.
Authors: Wu, Z. / Gogonea, V. / Lee, X. / Wagner, M.A. / Li, X.M. / Huang, Y. / Undurti, A. / May, R.P. / Haertlein, M. / Moulin, M. / Gutsche, I. / Zaccai, G. / Didonato, J.A. / Hazen, S.L.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apolipoprotein A-I
B: Apolipoprotein A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,990222
Polymers56,2412
Non-polymers159,748220
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A-I(1-242)


Mass: 28120.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 200 / Source method: obtained synthetically / Formula: C42H82NO8P / Details: POPC / Comment: phospholipid*YM
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C27H46O

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION SCATTERING / Number of used crystals: 1

-
Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: NUCLEAR REACTOR / Type: OTHER / Wavelength: 5 Å
DetectorDetector: AREA DETECTOR / Date: Oct 15, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 5 Å / Relative weight: 1
Reflection shellHighest resolution: 5 Å
Soln scatter

Conc. range: 2-4 / Data analysis software list: PRIMUS, GNOM, DAMMIN / Data reduction software list: ILL IN-HOUSE PACKAGE / Detector type: AREA / Num. of time frames: 3 / Sample pH: 7.4 / Source beamline: NEUTRON CAMERA FOR REACTOR SOURCE / Source beamline instrument: D22 (LOQ) / Source class: N / Source type: ILL / Temperature: 301 K / Type: neutron

IDBuffer nameMean guiner radius (nm)Mean guiner radius esd (nm)Protein length
1PBS IN 12% D2O5.130.0417.3
2PBS IN 42% D2O3.970.0515.2

-
Processing

Software
NameVersionClassification
ILLsoftwaredata collection
PRIMUSmodel building
GNOMmodel building
DAMMINmodel building
GROMACSrefinement
SASSIMrefinement
DEXANALrefinement
ILLsoftwaredata reduction
ILLsoftwaredata scaling
PRIMUSphasing
GNOMphasing
DAMMINphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 10960 0 14920
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT CHI SQUARE-FACTOR DEFINED BY THE DIFFERENCE BETWEEN THE CALCULATED AND EXPERIMENTAL SCATTERING INTENSITIES AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 2.4 NM-1 (PROTEIN) AND 2.1 NM-1 (LIPID).
Details: AN ALL ATOM COMPUTATIONAL MODEL WAS CONSTRUCTED BY COMBINING MOLELING WITH CONRAST VARIATION SANS, HYDROGEN-DEUTERIUM EXCHANGE (H/D-MS/MS), AND DISTANCE CONSTRAINTS FROM CROSS-LINKING, ...Details: AN ALL ATOM COMPUTATIONAL MODEL WAS CONSTRUCTED BY COMBINING MOLELING WITH CONRAST VARIATION SANS, HYDROGEN-DEUTERIUM EXCHANGE (H/D-MS/MS), AND DISTANCE CONSTRAINTS FROM CROSS-LINKING, FLUORESCENCE RESONANCE ENERGY TRANSFER AND ELECTRON SPIN RESONANCE. SANS LOW RESOLUTION STRUCTURES (12% AND 42% D2O) WERE USED AS SCAFFOLDS TO BUILD MOLECULAR MODELS FOR PROTEIN AND LIPID COMPONENTS OF NASCENT HDL. 256 MODELS WERE GENERATED AND ASSESSED USING GOODNESS-OF-FIT WITH BOTH SANS AND H/D-MS/MS DATA. THE NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING ALL ATOM STRUCTURE, AND WITH CORRECTIONS FOR WAVELENGTH SPREAD AND BEAM DIVERGENCE.
Entry fitting list: THE DOUBLE BELT MODEL (SEGREST JP, JBC 274, 31755 (1999))
Num. of conformers calculated: 256 / Num. of conformers submitted: 1 / Representative conformer: 1
Software author list: LINDAHL E, SALI A, DELANO WL, MERZEL F, RICHARDS RM, SVERGUN DI
Software list: GROMACS, MODELLER, PYMOL, SASSIM, YALE:VOLUME/ACCESS, PRIMUS, GNOM, DAMMIN

+
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