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- PDB-1nfo: APOLIPOPROTEIN E2 (APOE2, D154A MUTATION) -

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Basic information

Entry
Database: PDB / ID: 1nfo
TitleAPOLIPOPROTEIN E2 (APOE2, D154A MUTATION)
ComponentsAPOLIPOPROTEIN E2
KeywordsLIPID TRANSPORT / HEPARIN-BINDING / PLASMA PROTEIN / HDL / VLDL
Function / homology
Function and homology information


positive regulation of heparan sulfate proteoglycan binding / lipid transport involved in lipid storage / chylomicron remnant / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / metal chelating activity / triglyceride-rich lipoprotein particle clearance / lipoprotein particle ...positive regulation of heparan sulfate proteoglycan binding / lipid transport involved in lipid storage / chylomicron remnant / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / metal chelating activity / triglyceride-rich lipoprotein particle clearance / lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / regulation of amyloid-beta clearance / negative regulation of cholesterol biosynthetic process / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / very-low-density lipoprotein particle clearance / Chylomicron clearance / NMDA glutamate receptor clustering / acylglycerol homeostasis / response to caloric restriction / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / negative regulation of triglyceride metabolic process / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / regulation of amyloid fibril formation / regulation of behavioral fear response / regulation of protein metabolic process / high-density lipoprotein particle clearance / chylomicron / lipoprotein catabolic process / lipid transporter activity / high-density lipoprotein particle remodeling / phospholipid efflux / melanosome organization / multivesicular body, internal vesicle / AMPA glutamate receptor clustering / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / positive regulation of amyloid-beta clearance / very-low-density lipoprotein particle / positive regulation by host of viral process / low-density lipoprotein particle / lipoprotein biosynthetic process / positive regulation of CoA-transferase activity / protein import / high-density lipoprotein particle / negative regulation of blood coagulation / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / regulation of amyloid precursor protein catabolic process / cholesterol catabolic process / triglyceride homeostasis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of protein metabolic process / HDL remodeling / triglyceride metabolic process / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / cholesterol efflux / low-density lipoprotein particle receptor binding / artery morphogenesis / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / virion assembly / positive regulation of dendritic spine development / regulation of innate immune response / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / regulation of neuronal synaptic plasticity / antioxidant activity / lipoprotein particle binding / positive regulation of endocytosis / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / positive regulation of cholesterol efflux / regulation of protein-containing complex assembly / intracellular transport / fatty acid homeostasis / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / regulation of proteasomal protein catabolic process
Similarity search - Function
Apolipoprotein / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRupp, B. / Parkin, S.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Novel mechanism for defective receptor binding of apolipoprotein E2 in type III hyperlipoproteinemia.
Authors: Dong, L.M. / Parkin, S. / Trakhanov, S.D. / Rupp, B. / Simmons, T. / Arnold, K.S. / Newhouse, Y.M. / Innerarity, T.L. / Weisgraber, K.H.
History
DepositionJul 17, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN E2


Theoretical massNumber of molelcules
Total (without water)22,0641
Polymers22,0641
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.613, 53.671, 84.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein APOLIPOPROTEIN E2 / APOE2


Mass: 22064.021 Da / Num. of mol.: 1 / Fragment: 22KD RECEPTOR BINDING DOMAIN / Mutation: D154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2 / Organ: PLASMA / Production host: Escherichia coli (E. coli) / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Wilson, C., (1991) Science, 252, 1817. / PH range low: 5.3 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %PEG4001drop
320 mMsodium acetate1drop
40.2 %beta-n-octylglucopyranoside1drop
50.1 %beta-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / % possible obs: 94.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.0509
Reflection
*PLUS
Num. obs: 8964 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
ADSCdata collection
SHELXL-93phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHASING MODEL DERIVED FROM 1NFN

1nfn


Resolution: 2→8 Å / Num. parameters: 5267 / Num. restraintsaints: 4789 / Cross valid method: R-FREE / σ(F): 0
Details: RESIDUES 23 AND 24 ARE NOT WELL DEFINED AND THE BOND ANGLES ARE ON THE BORDERLINE OF THE ALLOWED REGIONS. CONSIDERING THE WEAK ELECTRON DENSITY THERE IS NO POINT IN ATTEMPTING TO ACCURATELY ...Details: RESIDUES 23 AND 24 ARE NOT WELL DEFINED AND THE BOND ANGLES ARE ON THE BORDERLINE OF THE ALLOWED REGIONS. CONSIDERING THE WEAK ELECTRON DENSITY THERE IS NO POINT IN ATTEMPTING TO ACCURATELY REFINE THESE TWO RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1248 10 %EVERY 10TH REFLECTION
all0.221 12485 --
obs0.206 -94.2 %-
Solvent computationSolvent model: 'SWAT' IN SHELXL93
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 0 143 1218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d2
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.103
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.052
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.047
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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