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- PDB-1f5y: NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BIND... -

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Entry
Database: PDB / ID: 1f5y
TitleNMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR
ComponentsLOW-DENSITY LIPOPROTEIN RECEPTOR
KeywordsLIPID BINDING PROTEIN / Beta hairpin / 3-10 helix / calcium binding
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 / clathrin heavy chain binding / negative regulation of receptor recycling / positive regulation of triglyceride biosynthetic process / intestinal cholesterol absorption / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle receptor activity / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / high-density lipoprotein particle clearance / regulation of protein metabolic process / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / negative regulation of amyloid fibril formation / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / receptor-mediated endocytosis / cholesterol metabolic process / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / apical part of cell / 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 / external side of plasma membrane / negative regulation of gene expression / 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
Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / 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. ...Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / 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 2. / EGF-like domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination
AuthorsKurniawan, N.D. / Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Smith, R.
Citation
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. / Bieri, S. / Brown, C.J. / Brereton, I.M. / Kroon, P.A. / Smith, R.
#1: Journal: Biochemistry / Year: 1998
Title: Calcium is Essential for the Structural Integrity of the Cysteine-Rich, Ligand-Binding Repeat of the Low-Density Lipoprotein Receptor
Authors: Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Lee, H.T. / Smith, R.
#2: Journal: Biochemistry / Year: 1998
Title: Folding, Calcium Binding, and Structural Characterization of a Concatemer of the First and Second Ligand-Binding Modules of the Low-Density Lipoprotein Receptor
Authors: Bieri, S. / Atkins, A.R. / Lee, H.T. / Winzor, D.J. / Smith, R. / Kroon, P.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Three-Dimensional Structure of a Cysteine-Rich Repeat from the Low-Density Lipoprotein Receptor
Authors: Daly, N.L. / Scanlon, M.J. / Djordjevic, J.T. / Kroon, P.A. / Smith, R.
#4: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of the Second Cysteine-Rich Repeat from the Human Low-Density Lipoprotein Receptor
Authors: Daly, N.L. / Djordjevic, J.T. / Kroon, P.A. / Smith, R.
History
DepositionJun 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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

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Assembly

Deposited unit
A: LOW-DENSITY LIPOPROTEIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3393
Polymers9,2591
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)20 / 50structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR / LDL RECEPTOR


Mass: 9258.997 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING MODULES 1-2
Source method: isolated from a genetically manipulated source
Details: LIGAND-BINDING MODULE CONCATEMER / Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Production host: Escherichia coli (E. coli) / 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
1112D-TOCSY
121DQF-COSY
1312D NOESY
142E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM LB1-2, 15 mM CaCl2, pH 5.595% H2O/5% D2O
21 mM LB1-2, 15 mM CaCl2, pH 5.599% D2O
Sample conditionsIonic strength: 0.045 / pH: 5.5 / Pressure: atmospheric atm / Temperature: 310 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
XwinNMR2BRUKERcollection
XEASY1.4ETH-Zurichdata analysis
DYANA1.5Guntertstructure solution
X-PLOR3.85Brungerrefinement
MOLMOL2.6Koradidata analysis
RefinementMethod: Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination
Software ordinal: 1
Details: NMR inputs: NOE total 889: 286 intra, 273 sequential, 184 medium, 146 long range; Others: 32 dihedral restraints, 13 h-bonds, 12 calcium coordination
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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