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- PDB-1i0u: SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-H... -

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Entry
Database: PDB / ID: 1i0u
TitleSOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR
ComponentsLOW DENSITY LIPOPROTEIN RECEPTOR
KeywordsLIPID BINDING PROTEIN / anti-parallel beta strands / calcium binding sites
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 / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / 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 / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / positive regulation of triglyceride biosynthetic process / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / low-density lipoprotein particle receptor activity / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / low-density lipoprotein particle binding / LDL clearance / response to caloric restriction / high-density lipoprotein particle clearance / regulation of protein metabolic process / phospholipid transport / lipoprotein catabolic process / low-density lipoprotein particle / cholesterol transport / cellular response to fatty acid / negative regulation of amyloid fibril formation / endolysosome membrane / negative regulation of low-density lipoprotein particle clearance / regulation of cholesterol metabolic process / artery morphogenesis / negative regulation of protein metabolic process / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / retinoid metabolic process / cholesterol metabolic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / endocytosis / apical part of cell / positive regulation of inflammatory response / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / negative regulation of gene expression / external side of plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / cell surface / Golgi apparatus / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site ...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 / : / Calcium-binding EGF domain / 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 domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / 1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation
AuthorsKurniawan, N.D. / Aliabadizadeh, K. / Brereton, I.M. / Kroon, P.A. / Smith, R.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: NMR structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-density lipoprotein receptor.
Authors: Kurniawan, N.D. / Aliabadizadeh, K. / Brereton, I.M. / Kroon, P.A. / Smith, R.
#1: Journal: Protein Sci. / Year: 2000
Title: NMR Structure of a Concatemer of the First and Second Ligand-Binding Modules of the Human Low-Density Lipoprotein Receptor
Authors: Kurniawan, N.D. / Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Smith, R.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An ...Title: An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components
Authors: Springer, T.A.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2001Provider: 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)9,0813
Polymers9,0011
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100Energy minimised average structure from 30 selected structure with lowest energy
Representative

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Components

#1: Protein LOW DENSITY LIPOPROTEIN RECEPTOR / LDL RECEPTOR


Mass: 9001.013 Da / Num. of mol.: 1 / Fragment: EGF-AB CONCATEMER(RESIDUES 314-395)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PGEX-4T; PET-30A+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA; BL21-DE3 / References: UniProt: P01130
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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
115HNHA
1232D NOESY
1342D NOESY
2412D NOESY
251DQF-COSY
3653D 15N-separated NOESY
NMR detailsText: 15N T1, T2, and NOE relaxations to obtain backbone dynamics information T1/T2 data were not used for structure refinement

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM EGF-AB, 20mM CaCl295% H2O/5% D2O
21mM EGF-AB, 20mM CaCl299% D2O
31mM 15N-EGF-AB, 20mM CaCl295% H2O/5% D2O
41.5mM EGF-A, 20mM CaCl299% D2O
51.5mM EGF-A, 20mM CaCl295% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.065.5ambient 310 K
20.065.5ambient 283 K
30.065.5ambient 295 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
XwinNMR2.6Brukercollection
Sparky3.95T. Goddard & D. G. Knellerprocessing
DYANA1.5P. Guntertstructure solution
X-PLOR3.85A. Brungerrefinement
MOLMOL2.6R. Koradidata analysis
RefinementMethod: 1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation
Software ordinal: 1
Details: The structures are based on: 874 NOE restraints, 64 phi dihedral angles, 14 chi1 dihedral angles, 14 hydrogen bonds, 9 calcium ion ligand restraints
NMR ensembleConformer selection criteria: Energy minimised average structure from 30 selected structure with lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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