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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 / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport / aorta morphogenesis / amyloid-beta clearance by transcytosis / regulation of extracellular matrix disassembly / clathrin heavy chain binding / lipid transport involved in lipid storage / 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 / negative regulation of smooth muscle cell migration / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / positive regulation of lipoprotein transport / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle remodeling / low-density lipoprotein particle receptor activity / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / Chylomicron remodeling / lipid transporter activity / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of amyloid fibril formation / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / regulation of protein metabolic process / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / AMPA glutamate receptor clustering / lipoprotein catabolic process / melanosome organization / multivesicular body, internal vesicle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / transcytosis / high-density lipoprotein particle assembly / plasma membrane protein complex / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / astrocyte activation involved in immune response / synaptic transmission, cholinergic / apoptotic cell clearance / HDL remodeling / negative regulation of endothelial cell migration / cargo receptor activity / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / lipoprotein transport / scavenger receptor activity / lysosomal transport / Scavenging by Class A Receptors / triglyceride metabolic process / positive regulation of dendritic spine development / 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. ...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. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / 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 1. / EGF-like domain signature 2. / 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Has protein modificationY

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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)
10.157.45ambient 298 K
20.057.45ambient 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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