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- PDB-1gs9: Apolipoprotein E4, 22k domain -

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Basic information

Entry
Database: PDB / ID: 1gs9
TitleApolipoprotein E4, 22k domain
ComponentsAPOLIPOPROTEIN E
KeywordsLIPID BINDING PROTEIN / LIPID TRANSPORT / HEPARIN-BINDING / PLASMA
Function / homology
Function and homology information


chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle / regulation of amyloid-beta clearance / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle remodeling / Chylomicron clearance / negative regulation of triglyceride metabolic process / response to caloric restriction / acylglycerol homeostasis / NMDA glutamate receptor clustering / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / regulation of amyloid fibril formation / regulation of protein metabolic process / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / melanosome organization / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / positive regulation by host of viral process / very-low-density lipoprotein particle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / cholesterol transfer activity / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / protein import / negative regulation of blood coagulation / high-density lipoprotein particle / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / synaptic transmission, cholinergic / heparan sulfate proteoglycan binding / negative regulation of cholesterol biosynthetic process / amyloid precursor protein metabolic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / negative regulation of protein metabolic process / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding / triglyceride metabolic process / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / locomotory exploration behavior / regulation of neuronal synaptic plasticity / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / lipoprotein particle binding / positive regulation of endocytosis / antioxidant activity / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / positive regulation of cholesterol efflux / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / synaptic cleft / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVerderame, J.R. / Kantardjieff, K. / Segelke, B. / Weisgraber, K. / Rupp, B.
CitationJournal: To be Published
Title: Crystal Structure of the 22K Domain of Human Apolipoprotein E4
Authors: Verderame, J.R. / Kantardjieff, K. / Segelke, B. / Weisgraber, K. / Rupp, B.
History
DepositionJan 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX THE HELICES ASSIGNED 1 TO 5 IN THIS ENTRY ARE LABELED IN THE APOE LITERATURE AS 1,1',2,3,4, ... HELIX THE HELICES ASSIGNED 1 TO 5 IN THIS ENTRY ARE LABELED IN THE APOE LITERATURE AS 1,1',2,3,4, WITH 1' BEING A SHORT CONNECTING HELIX BETWEEN 1 AND 2 OF THE FOUR HELIX BUNLDE CONSISTING OF HELICES 1,2,3 AND 4.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN E


Theoretical massNumber of molelcules
Total (without water)19,3521
Polymers19,3521
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.511, 53.089, 73.372
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 E / APOE4


Mass: 19351.857 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 1-165 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: OBTAINED THROUGH PROTEOLYTIC CLEAVAGE OF FULL LENGTH APOE4 (299 RESIDUES) DURING CRYSTALLIZATION
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P02649
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVARIANT: CYS (112) ARG. APOE4 IS A NATURALLY OCCURING ALLELIC VARIANT OF E4, THE SECOND MOST COMMON ...VARIANT: CYS (112) ARG. APOE4 IS A NATURALLY OCCURING ALLELIC VARIANT OF E4, THE SECOND MOST COMMON ISOFORM AFTER E3
Sequence detailsARG A 112, E4 ALLELE, RESIDUES 1-21 ABSENT FROM ELETRON DENSITY

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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: 2.56 Å3/Da / Density % sol: 49.9 %
Crystal growpH: 5.6
Details: 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, ...Details: 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, THIRD ORTHOGONAL CRYSTAL FORM OF APOE (ORTHO-3)

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 1999 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→20.9 Å / Num. obs: 20168 / % possible obs: 99.97 % / Redundancy: 7.7 % / Rsym value: 0.035 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BZ4

1bz4


Resolution: 1.7→20.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.415 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THIS IS THE 4TH KNOWN (3RD ORTHORHOMBIC) CRYSTAL FORM OF APOLIPOPROTEIN E. COMPARE 1BZ4, 1OR2, 1OR3, HIGHEST RESOLUTION E4 VARIANT. RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THIS IS THE 4TH KNOWN (3RD ORTHORHOMBIC) CRYSTAL FORM OF APOLIPOPROTEIN E. COMPARE 1BZ4, 1OR2, 1OR3, HIGHEST RESOLUTION E4 VARIANT. RESIDUES 1-21 ARE ABSENT FROM ELECTRON DENSITY AS OBSERVED IN OTHER CRYSTAL FORMS OF APOE. THE C-TERMINAL BECOMES UNDEFINED PAST RESIDUE 165, ALTHOUGH WEA DENSITY INDICATES THAT MORE RESIDUES COULD BE PRESENT. IT IS NOT KNOWN HOW MANY RESIDUES PAST 165 THIS CONSTRUCT CONTAINS AS IT FORMED IN SITU IN THE CRYSTALLIZATION DROPS THROUGH UNKNOWN PROTOLYTICAL CLEAVAGE FROM 299 RESIDUE, FULL LENGTH NAT APOE4. IT IS KNOWN THAT THROMBIN CLEAVAGE LEAVES A 191 RESIDUE 22KD FRAGMENT. RESIDUES IN FLEXIBLE LOOP REGION 84-89 ARE WEAKLY DEFINED AND EXHIBIT HIGH B-FACTORS, AS COMMONLY OBSERVED IN THE OTHER APOE CRYSTAL FORMS. REGION 124- 126 LINKING HELIX 3 AND 4 APPEARS TO HAVE MULTIPLE CONFORMATIONS INCLUDING THE BACKBONE BUT HAS BEEN MODELLED WITH SINGLE CHAIN ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1045 5.2 %RANDOM
Rwork0.218 ---
obs0.219 19116 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---1 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 223 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9741635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1613143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59215255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02916
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.3634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.5149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.335
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.532
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2372716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35431140
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5073506
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1114495
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rfree0.429 38
Rwork0.304 696

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