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- PDB-1f8z: NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1f8z
TitleNMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR
ComponentsLOW-DENSITY LIPOPROTEIN RECEPTOR
KeywordsLIPID BINDING PROTEIN / LDL receptor / ligand-binding domain / calcium-binding / familial hypercholesterolemia
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / low-density lipoprotein particle receptor activity / negative regulation of low-density lipoprotein particle clearance / Chylomicron clearance / response to caloric restriction / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / sorting endosome / lipoprotein particle binding / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / 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. / : ...: / 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
Similarity search - Domain/homology
Low-density lipoprotein receptor
Similarity search - Component
MethodSOLUTION NMR / Structure determination by Torsion angle dynamics, Molecular dynamics
AuthorsClayton, D.J. / Brereton, I.M. / Kroon, P.A. / Smith, R.
CitationJournal: FEBS Lett. / Year: 2000
Title: Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities.
Authors: Clayton, D. / Brereton, I.M. / Kroon, P.A. / Smith, R.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOW-DENSITY LIPOPROTEIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4332
Polymers4,3931
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 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein/peptide LOW-DENSITY LIPOPROTEIN RECEPTOR


Mass: 4392.759 Da / Num. of mol.: 1 / Fragment: SIXTH LIGAND-BINDING MODULE / Source method: obtained synthetically / Details: Peptide synthesis - based on the human sequence / References: UniProt: P01130
#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
1112D NOESY
121DQF-COSY
132E-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate90% H2O/10% D2O
23 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate100% D2O
Sample conditionsIonic strength: 10 mM / 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 DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBrukercollection
AURELIABrukerprocessing
XEASYXia & Bartelsprocessing
DYANA1.5Peter Guntertstructure solution
X-PLOR3.1Axel Brungerstructure solution
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: Structure determination by Torsion angle dynamics, Molecular dynamics
Software ordinal: 1
Details: Structures are based on 552 distance constraints, 18 backbone angle restraints and 14 sidechain angle restraints
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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