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- PDB-1d2l: NMR SOLUTION STRUCTURE OF COMPLEMENT-LIKE REPEAT CR3 FROM THE LOW... -

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Basic information

Entry
Database: PDB / ID: 1d2l
TitleNMR SOLUTION STRUCTURE OF COMPLEMENT-LIKE REPEAT CR3 FROM THE LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN (LRP). EVIDENCE FOR SPECIFIC BINDING TO THE RECEPTOR BINDING DOMAIN OF HUMAN ALPHA-2 MACROGLOBULIN
ComponentsLIPOPROTEIN RECEPTOR RELATED PROTEIN
KeywordsSIGNALING PROTEIN / LIGAND BINDING / CALCIUM BINDING / COMPLEMENT-LIKE REPEAT / RECEPTOR
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 / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / regulation of extracellular matrix disassembly / positive regulation of amyloid-beta clearance / amyloid-beta clearance by cellular catabolic process / scavenger receptor activity / heparan sulfate proteoglycan binding / plasma membrane protein complex / transcytosis / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / lysosomal transport / microtubule organizing center / retinoid metabolic process / lipoprotein transport / negative regulation of Wnt signaling pathway / positive regulation of endocytosis / negative regulation of SMAD protein signal transduction / enzyme-linked receptor protein signaling pathway / amyloid-beta clearance / apolipoprotein binding / transport across blood-brain barrier / positive regulation of cholesterol efflux / Scavenging of heme from plasma / Retinoid metabolism and transport / phagocytosis / 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 / signaling receptor activity / amyloid-beta binding / positive regulation of protein binding / basolateral plasma membrane / receptor complex / early endosome / 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 / Low-density lipoprotein-receptor YWTD domain ...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 / MOLECULAR DYNAMICS ENERGY MINIMIZATION
AuthorsDolmer, K. / Huang, W. / Gettins, P.G.W.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: NMR solution structure of complement-like repeat CR3 from the low density lipoprotein receptor-related protein. Evidence for specific binding to the receptor binding domain of human alpha(2)-macroglobulin.
Authors: Dolmer, K. / Huang, W. / Gettins, P.G.
History
DepositionSep 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / 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_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPOPROTEIN RECEPTOR RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9922
Polymers4,9521
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide LIPOPROTEIN RECEPTOR RELATED PROTEIN


Mass: 4952.353 Da / Num. of mol.: 1 / Fragment: COMPLEMENT-LIKE REPEAT 3 (CR3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PGEX-2T / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED TOCSY
1213D 13C-SEPARATED TOCSY
1313D 15N-SEPARATED NOESY
1413D 13C-SEPARATED NOESY
151HBHA(CO)NH
161CBCA(CO)NH
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. 20 STRUCTURES IN THE DEPOSITION WERE FITTED BY FITTING STRUCTURES 2-20 TO THE FIRST, USING PROFIT V1.8 (MCLACHLAN, A. D., ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. 20 STRUCTURES IN THE DEPOSITION WERE FITTED BY FITTING STRUCTURES 2-20 TO THE FIRST, USING PROFIT V1.8 (MCLACHLAN, A. D., 1982 ACTA. CRYST.A38, 871-3) AS IMPLEMENTED IN THE PROGRAM PROFIT (MARTIN, A. C. R.,HTTP:// WWW.BIOCHEM.UCL.AC.UK/~MARTIN/PROGRAMS/#PROFIT)

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Sample preparation

DetailsContents: 2 MM CR3 U-15N,13C 20 MM NA-D3-ACETATE PH 5.5 10 MM CACL 90% H2O, 10% D2O
Sample conditionsIonic strength: 20 mM NA-D3-ACETATE, 10 mM CACL2 / pH: 5.5 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
SYBYL6.3TRIPOS INC.processing
DYANA1.5GUNTERT, P., MUMENTHALER, C., AND WUTHRICH, K. (1997) JMB 273, 283-98structure solution
Amber5CASE, D. A., ET AL. (1997) AMBER 5, UNIV. OF CALIFORNIA, SAN FRANCISCO, UNPUBLISHEDrefinement
ProFit1.8McLachlan, A. D. (1982 Acta. Cryst. A38, 871-3)structure solution
RefinementMethod: MOLECULAR DYNAMICS ENERGY MINIMIZATION / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 602 NOE CONSTRAINTS, 9 DISTANCE CONSTRAINTS FOR THE CALCIUM BINDING SITE, 3 DISULFIDE BRIDGES, 10 HYDROGEN BONDS AND FIVE DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 20

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