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- PDB-3r2p: 2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apol... -

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Basic information

Entry
Database: PDB / ID: 3r2p
Title2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apolipoprotein A-I Reveals the Assembly of HDL by Dimerization.
ComponentsApolipoprotein A-IApolipoprotein AI
KeywordsLIPID TRANSPORT / amphipathic alpha-helix / major protein of high density lipoprotein (HDL) / lipid binding / plasma
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 / regulation of intestinal cholesterol absorption / negative regulation of response to cytokine stimulus / protein oxidation / 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 / regulation of intestinal cholesterol absorption / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / high-density lipoprotein particle binding / cholesterol import / ABC transporters in lipid homeostasis / negative regulation of heterotypic cell-cell adhesion / blood vessel endothelial cell migration / apolipoprotein receptor binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / apolipoprotein A-I receptor binding / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / phosphatidylcholine metabolic process / positive regulation of phospholipid efflux / lipid storage / phospholipid homeostasis / Chylomicron assembly / positive regulation of cholesterol metabolic process / high-density lipoprotein particle remodeling / high-density lipoprotein particle clearance / phospholipid efflux / cholesterol transfer activity / reverse cholesterol transport / cholesterol transport / chemorepellent activity / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / high-density lipoprotein particle / endothelial cell proliferation / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / cholesterol binding / negative regulation of interleukin-1 beta production / positive regulation of Rho protein signal transduction / negative chemotaxis / adrenal gland development / cholesterol biosynthetic process / endocytic vesicle / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / positive regulation of phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / Retinoid metabolism and transport / 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 / regulation of protein phosphorylation / phospholipid binding / Heme signaling / PPARA activates gene expression / 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 / collagen-containing extracellular matrix / secretory granule lumen / blood microparticle / protein stabilization / early endosome / 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 / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #20 / Apolipoprotein / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2045 Å
AuthorsMei, X. / Atkinson, D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of C-terminal Truncated Apolipoprotein A-I Reveals the Assembly of High Density Lipoprotein (HDL) by Dimerization.
Authors: Mei, X. / Atkinson, D.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Structure summary
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein A-I


Theoretical massNumber of molelcules
Total (without water)21,6561
Polymers21,6561
Non-polymers00
Water68538
1
A: Apolipoprotein A-I

A: Apolipoprotein A-I


Theoretical massNumber of molelcules
Total (without water)43,3122
Polymers43,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7850 Å2
ΔGint-74 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.333, 30.178, 69.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y, z and x, y+1, Z

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Components

#1: Protein Apolipoprotein A-I / Apolipoprotein AI / Apo-AI / ApoA-I / Apolipoprotein A1 / Apolipoprotein A-I(1-242)


Mass: 21656.234 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP 25-208)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Plasmid: pDEST-His6-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: P02647
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.15M potassium bromide, 30% PEG 2000 MME, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.91994 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91994 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 11930 / Num. obs: 11930 / % possible obs: 98.2 % / Observed criterion σ(F): 2.95 / Observed criterion σ(I): 2.95 / Redundancy: 6.4 % / Biso Wilson estimate: 37.46 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.017
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.95 / Num. unique all: 532 / % possible all: 89.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.autoMR: 1.6.2_432)model building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.2_432phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Use the Se-Met derivative to obtain the starting model from SAD experiment.

Resolution: 2.2045→34.788 Å / SU ML: 0.33 / Isotropic thermal model: Mixed individual ADP with TLS / σ(F): 0 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1191 10 %Random
Rwork0.2304 ---
all0.2356 11905 --
obs0.2356 11905 97.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.738 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 63.7952 Å2
Baniso -1Baniso -2Baniso -3
1-29.7755 Å2-0 Å2-0 Å2
2---7.8408 Å2-0 Å2
3----21.9347 Å2
Refinement stepCycle: LAST / Resolution: 2.2045→34.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 0 38 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071512
X-RAY DIFFRACTIONf_angle_d0.9582036
X-RAY DIFFRACTIONf_dihedral_angle_d15.182597
X-RAY DIFFRACTIONf_chiral_restr0.063216
X-RAY DIFFRACTIONf_plane_restr0.006268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2045-2.29280.40771190.31741071119090
2.2928-2.39710.33271250.31471129125496
2.3971-2.52350.38971340.29491198133299
2.5235-2.68150.40391300.28221174130499
2.6815-2.88850.36941320.257611911323100
2.8885-3.1790.30031350.264512131348100
3.179-3.63850.29661350.226512101345100
3.6385-4.58250.24651370.185812361373100
4.5825-34.79230.21151440.20571292143697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09831.2873-0.0630.40770.61411.0623-0.0298-0.1037-0.0480.1332-0.0261-0.04680.0586-0.02790.01560.39220.0567-0.03710.23070.00120.3004-29.3098-6.66-29.4704
21.39920.84190.5310.60241.25971.23720.001-0.51060.4050.2537-0.34120.1984-0.1468-0.50150.22680.44030.1640.03760.3768-0.02080.3744-35.02730.8897-16.3313
32.77261.80270.79991.27860.81842.6795-0.06220.91020.5465-0.41710.21060.62020.4491-0.1734-0.12980.68320.0308-0.02340.5182-0.06040.7208-0.963121.79865.4763
42.43881.5867-1.94511.1174-1.14171.70780.4472-0.49860.3120.54950.00460.149-0.28880.4394-0.18970.44050.0356-0.04570.3234-0.00760.320732.551639.7184-18.7399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:76)
2X-RAY DIFFRACTION2(chain A and resid 77:119)
3X-RAY DIFFRACTION3(chain A and resid 120:144)
4X-RAY DIFFRACTION4(chain A and resid 145:183)

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