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- PDB-1cr8: LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8 -

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Basic information

Entry
Database: PDB / ID: 1cr8
TitleLOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8
ComponentsPROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)
KeywordsLIPID BINDING PROTEIN / RECEPTOR / LIGAND BINDING / CALCIUM BINDING / LDLR / LRP
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / regulation of phospholipase A2 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 / negative regulation of smooth muscle cell migration ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / regulation of phospholipase A2 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 / negative regulation of smooth muscle cell migration / aorta morphogenesis / regulation of cholesterol transport / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / regulation of extracellular matrix disassembly / low-density lipoprotein particle receptor activity / amyloid-beta clearance by cellular catabolic process / scavenger receptor activity / plasma membrane protein complex / positive regulation of amyloid-beta clearance / transcytosis / heparan sulfate proteoglycan binding / lysosomal transport / apoptotic cell clearance / astrocyte activation involved in immune response / microtubule organizing center / cargo receptor activity / retinoid metabolic process / lipoprotein transport / negative regulation of SMAD protein signal transduction / enzyme-linked receptor protein signaling pathway / negative regulation of Wnt signaling pathway / apolipoprotein binding / positive regulation of endocytosis / amyloid-beta clearance / transport across blood-brain barrier / positive regulation of cholesterol efflux / Scavenging of heme from plasma / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / lipid metabolic process / receptor internalization / cellular response to amyloid-beta / endocytic vesicle membrane / positive regulation of protein binding / signaling receptor activity / amyloid-beta binding / basolateral plasma membrane / early endosome / receptor complex / lysosomal membrane / negative regulation of gene expression / focal adhesion / calcium ion binding / protein-containing complex binding / Golgi apparatus / RNA binding / membrane / nucleus / plasma membrane
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / Complement Clr-like EGF domain / Complement Clr-like EGF-like / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DYNAMICS ANNEALING
AuthorsHuang, W. / Dolmer, K. / Gettins, P.G.W.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: NMR solution structure of complement-like repeat CR8 from the low density lipoprotein receptor-related protein.
Authors: Huang, W. / Dolmer, K. / Gettins, P.G.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6962
Polymers4,6561
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein/peptide PROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)


Mass: 4656.135 Da / Num. of mol.: 1 / Fragment: COMPLEMENT REPEAT 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER, PLACENTA / Plasmid: PGEX-2T / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07954
#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
111NOESY-HSQC
121TOCSY-HSQC
131(H)CCH-
NMR detailsText: FIRST. N-15 EDITED TOCSY-HSQC, NOESY-HSQC, HNHA C-13 EDITED HCCH-TOCSY, HCCH- NOESY, TRIPLE RESONANCE HNCA, HBHA(CO)NH

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Sample preparation

Sample conditionsIonic strength: 0.05 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
RefinementMethod: DYNAMICS ANNEALING / Software ordinal: 1 / Details: ENERGY MINIMIZATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 20

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