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- PDB-1av1: CRYSTAL STRUCTURE OF HUMAN APOLIPOPROTEIN A-I -

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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 / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / 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 / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / cholesterol import / high-density lipoprotein particle binding / blood vessel endothelial cell migration / ABC transporters in lipid homeostasis / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I 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 / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle clearance / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / phospholipid homeostasis / cholesterol transfer activity / chemorepellent activity / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / low-density lipoprotein particle / lipoprotein biosynthetic process / positive regulation of CoA-transferase activity / cholesterol transport / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / cholesterol efflux / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / cholesterol binding / adrenal gland development / negative chemotaxis / positive regulation of Rho protein signal transduction / cholesterol biosynthetic process / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / Scavenging of heme from plasma / Retinoid metabolism and transport / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / cholesterol metabolic process / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Heme signaling / regulation of protein phosphorylation / 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) / extracellular vesicle / Platelet degranulation / amyloid-beta binding / cytoplasmic vesicle / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / early endosome / protein stabilization / receptor ligand activity / G protein-coupled receptor signaling pathway / 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-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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 %

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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

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