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- PDB-2kny: Fusion construct of CR17 from LRP-1 and ApoE residues 130-149 -

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Basic information

Entry
Database: PDB / ID: 2kny
TitleFusion construct of CR17 from LRP-1 and ApoE residues 130-149
ComponentsLRP-1, linker, Apo-E
KeywordsMETAL BINDING PROTEIN / LRP / ApoE / Lipoprotein receptor / ligand binding module / complement repeat / Calcium / Cell membrane / Coated pit / Cytoplasm / Developmental protein / Disulfide bond / EGF-like domain / Endocytosis / Glycoprotein / Membrane / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Transmembrane / Protein binding
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis / negative regulation of smooth muscle cell migration / regulation of cholesterol transport / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / low-density lipoprotein particle receptor activity / regulation of extracellular matrix disassembly / 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 / amyloid-beta clearance by cellular catabolic process / 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 / scavenger receptor activity / 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 / plasma membrane protein complex / 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 / transcytosis / 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 / astrocyte activation involved in immune response / regulation of amyloid precursor protein catabolic process / apoptotic cell clearance / positive regulation of membrane protein ectodomain proteolysis / cargo receptor activity / HDL remodeling / retinoid metabolic process / negative regulation of endothelial cell migration / lysosomal transport / Scavenging by Class A Receptors / negative regulation of protein metabolic process / artery morphogenesis / cholesterol efflux / microtubule organizing center / lipoprotein transport / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / : / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Apolipoprotein E / Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsGuttman, M. / Komives, E.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the minimal interface between ApoE and LRP.
Authors: Guttman, M. / Prieto, J.H. / Handel, T.M. / Domaille, P.J. / Komives, E.A.
History
DepositionSep 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LRP-1, linker, Apo-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4402
Polymers8,3991
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 328structures with the least restraint violations
RepresentativeModel #9closest to the average

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Components

#1: Protein LRP-1, linker, Apo-E / LRP / Alpha-2-macroglobulin receptor / A2MR / Apolipoprotein E receptor / APOER / Low-density ...LRP / Alpha-2-macroglobulin receptor / A2MR / Apolipoprotein E receptor / APOER / Low-density lipoprotein receptor-related protein 1 85 kDa subunit / LRP-85 / Low-density lipoprotein receptor-related protein 1 515 kDa subunit / LRP-515 / Low-density lipoprotein receptor-related protein 1 intracellular domain / LRPICD


Mass: 8399.437 Da / Num. of mol.: 1
Fragment: Fusion of LRP UNP residues 2770-2817 and Apo-E UNP residues 147-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP1, A2MR, APR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q07954, UniProt: P02649
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2212D 1H-13C HSQC
2313D CBCA(CO)NH
2413D C(CO)NH
2513D HNCO
2623D (H)CCH-TOCSY
2713D 1H-15N NOESY
2823D 1H-13C NOESY
2923D (H)CCH-COSY
11052D 1H-15N HSQC
11152D 1H-13C HSQC
11253D CBCA(CO)NH
11353D HNCO
11453D (H)CCH-COSY
11542D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM [U-99% 2H] HEPES-1, 50 mM sodium chloride-2, 3 mM sodium azide-3, 5 mM CALCIUM ION-4, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-5, 90% H2O/10% D2O90% H2O/10% D2O
220 mM [U-99% 2H] HEPES-6, 50 mM sodium chloride-7, 3 mM sodium azide-8, 5 mM CALCIUM ION-9, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-10, 100% D2O100% D2O
320 mM [U-99% 2H] HEPES-11, 50 mM sodium chloride-12, 3 mM sodium azide-13, 5 mM CALCIUM ION-14, 0.8 mM [U-99% 15N] entity_1-15, 90% H2O/10% D2O90% H2O/10% D2O
420 mM [U-99% 2H] HEPES-16, 150 mM sodium chloride-17, 3 mM sodium azide-18, 2 mM [U-99% 2H] EDTA-19, 0.5 mM [U-99% 15N] entity_2-20, 90% H2O/10% D2O90% H2O/10% D2O
520 mM [U-99% 2H] HEPES-21, 150 mM sodium chloride-22, 3 mM sodium azide-23, 2 mM [U-99% 2H] EDTA-24, 0.5 mM [U-99% 13C; U-99% 15N] entity_2-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMHEPES-1[U-99% 2H]1
50 mMsodium chloride-21
3 mMsodium azide-31
5 mMCALCIUM ION-41
0.8 mMentity_1-5[U-99% 13C; U-99% 15N]1
20 mMHEPES-6[U-99% 2H]2
50 mMsodium chloride-72
3 mMsodium azide-82
5 mMCALCIUM ION-92
0.8 mMentity_1-10[U-99% 13C; U-99% 15N]2
20 mMHEPES-11[U-99% 2H]3
50 mMsodium chloride-123
3 mMsodium azide-133
5 mMCALCIUM ION-143
0.8 mMentity_1-15[U-99% 15N]3
20 mMHEPES-16[U-99% 2H]4
150 mMsodium chloride-174
3 mMsodium azide-184
2 mMEDTA-19[U-99% 2H]4
0.5 mMentity_2-20[U-99% 15N]4
20 mMHEPES-21[U-99% 2H]5
150 mMsodium chloride-225
3 mMsodium azide-235
2 mMEDTA-24[U-99% 2H]5
0.5 mMentity_2-25[U-99% 13C; U-99% 15N]5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 7.45 ambient 298 K
20.05 7.45 ambient 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Azara2.7Boucherprocessing
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.2Linge, O'Donoghue and Nilgeschemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeGoddardchemical shift assignment
NMRPipeGoddarddata analysis
NMRPipeGoddardpeak picking
TALOSCornilescu, Delaglio and Baxrefinement
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2014 / NOE intraresidue total count: 217 / NOE long range total count: 384 / NOE medium range total count: 248 / NOE sequential total count: 289 / Hydrogen bond constraints total count: 6 / Protein phi angle constraints total count: 39 / Protein psi angle constraints total count: 39
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 328 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum torsion angle constraint violation: 4.835 ° / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.0459 Å / Distance rms dev error: 0.0038 Å

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