[English] 日本語
Yorodumi
- PDB-1av1: CRYSTAL STRUCTURE OF HUMAN APOLIPOPROTEIN A-I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1av1
TitleCRYSTAL STRUCTURE OF HUMAN APOLIPOPROTEIN A-I
ComponentsAPOLIPOPROTEIN A-I
KeywordsLIPID TRANSPORT / LIPOPROTEIN / CHOLESTEROL METABOLISM / ATHEROSCLEROSIS / HDL / LCAT-ACTIVATION
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-I / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 4 Å
AuthorsBorhani, D.W. / Rogers, D.P. / Engler, J.A. / Brouillette, C.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation.
Authors: Borhani, D.W. / Rogers, D.P. / Engler, J.A. / Brouillette, C.G.
#1: Journal: Biochemistry / Year: 1997
Title: Structural Analysis of Apolipoprotein A-I: Limited Proteolysis of Methionine-Reduced and-Oxidized Lipid-Free and Lipid-Bound Human Apo A-I
Authors: Roberts, L.M. / Ray, M.J. / Shih, T.W. / Hayden, E. / Reader, M.M. / Brouillette, C.G.
#2: Journal: Biochemistry / Year: 1997
Title: Truncation of the Amino Terminus of Human Apolipoprotein A-I Substantially Alters Only the Lipid-Free Conformation
Authors: Rogers, D.P. / Brouillette, C.G. / Engler, J.A. / Tendian, S.W. / Roberts, L. / Mishra, V.K. / Anantharamaiah, G.M. / Lund-Katz, S. / Phillips, M.C. / Ray, M.J.
#3: Journal: Biochim.Biophys.Acta / Year: 1995
Title: Structural Models of Human Apolipoprotein A-I
Authors: Brouillette, C.G. / Anantharamaiah, G.M.
History
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Refinement description / Category: diffrn_source / pdbx_database_status / software
Item: _diffrn_source.type / _pdbx_database_status.process_site / _software.name
Revision 1.4Feb 7, 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 A-I
B: APOLIPOPROTEIN A-I
C: APOLIPOPROTEIN A-I
D: APOLIPOPROTEIN A-I


Theoretical massNumber of molelcules
Total (without water)93,7624
Polymers93,7624
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32020 Å2
ΔGint-254 kcal/mol
Surface area51470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.470, 113.870, 196.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.231719, -0.855967, -0.462202), (-0.856755, -0.045469, 0.513715), (-0.460739, 0.515028, -0.722818)76.144, 41.285, 50.605
2given(0.057013, 0.997283, -0.04664), (0.997171, -0.059174, -0.046348), (-0.048982, -0.043865, -0.997836)17.832, -16.343, 53.159
3given(-0.846149, -0.118168, 0.51968), (-0.159004, -0.874725, -0.457792), (0.508674, -0.469991, 0.721359)60.986, 54.797, -2.877

-
Components

#1: Protein
APOLIPOPROTEIN A-I / APO A-I


Mass: 23440.559 Da / Num. of mol.: 4 / Fragment: LIPID-BINDING DOMAIN / Mutation: N-TERMINAL MET, DEL(1-43)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02647

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 5.83 Å3/Da / Density % sol: 72 %
Description: DATA WERE EXCLUDED ON A RESOLUTION-DEPENDENT BASIS FOR ALL RESOLUTION SHELLS IN WHICH THE FOR FULLY-RECORDED REFLECTIONS IN THAT SHELL WAS LESS THAN 2.5.
Crystal growTemperature: 277 K / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.2 M NA CITRATE, 100 MM HEPES, PH 7.5 AT 4 DEGREES CELSIUS. CRYSTALS WERE STABILIZED IN 1.4 M NA CITRATE, 100 MM HEPES, PH 7.5., temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
Conc.: 1.2 M / Common name: sodium citrate

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 24, 1996 / Details: DUAL SLITS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 16089 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 3.7
Reflection shellResolution: 4→4.22 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 0.9 / Rsym value: 0.732 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50 %

-
Processing

Software
NameVersionClassification
HASSPmodel building
X-PLOR3.843model building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
HASSPphasing
X-PLOR3.843phasing
RefinementMethod to determine structure: MIRAS / Resolution: 4→27 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: 24 (GROUPED) THERMAL FACT / Cross valid method: THROUGHOUT / σ(F): 2
Details: DATA USED IN REFINEMENT WERE SHARPENED BY APPLICATION OF AN ARTIFICIAL TEMPERATURE FACTOR (-70. A**2).
RfactorNum. reflection% reflectionSelection details
Rfree0.428 785 5 %RANDOM
Rwork0.382 ---
obs0.382 15543 81.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-119.984 Å20 Å20 Å2
2--138.351 Å20 Å2
3---128.014 Å2
Refinement stepCycle: LAST / Resolution: 4→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 0 0 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 4→4.18 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.462 52 5 %
Rwork0.43 946 -
obs--42.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43
LS refinement shell
*PLUS
Rfactor Rwork: 0.43

+
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