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- PDB-1hj7: NMR study of a pair of LDL receptor Ca2+ binding epidermal growth... -

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Basic information

Entry
Database: PDB / ID: 1hj7
TitleNMR study of a pair of LDL receptor Ca2+ binding epidermal growth factor-like domains, 20 structures
ComponentsLDL RECEPTOR
KeywordsCELL-SURFACE RECEPTOR / CALCIUM-BINDING / EGF-LIKE DOMAIN / MODULE / APO-E / APO-B / LDL / VLDL
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
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. / : ...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. / : / 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 / 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 / simulated annealing
AuthorsSaha, S. / Handford, P.A. / Campbell, I.D. / Downing, A.K.
Citation
Journal: Structure / Year: 2001
Title: Solution Structure of the Ldl Receptor Egf-Ab Pair: A Paradigm for the Assembly of Tandem Calcium Binding Egf Domains
Authors: Saha, S. / Boyd, J. / Werner, J.M. / Knott, V. / Handford, P.A. / Campbell, I.D. / Downing, A.K.
#1: Journal: Methods Mol.Biol. / Year: 2002
Title: The Use of Dipolar Couplings for the Structure Refinement of a Pair of Calcium-Binding Egf Domains.
Authors: Boyd, J. / Campbell, I.D. / Downing, A.K.
#2: Journal: Biochemistry / Year: 2001
Title: The First Epidermal Growth Factor-Like Domain of the Low-Density Lipoprotein Receptor Contains a Noncanonical Calcium Binding Site
Authors: Malby, S. / Pickering, R. / Saha, S. / Smallridge, R.S. / Linse, S. / Downing, A.K.
History
DepositionJan 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Feb 14, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LDL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9113
Polymers8,8311
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 / 280NO NOE, 3JHN OR 1JHN CONSTRAINTS VIOLATED BY > 0.5 A, 5 DEGREES OR 2 HERTZ
RepresentativeModel #1

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Components

#1: Protein LDL RECEPTOR


Mass: 8830.804 Da / Num. of mol.: 1
Fragment: CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR, RESIDUES 293-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: TRANSMEMBRANE / Gene: LDLR / Plasmid: PQE30 (QIAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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
1111H-NOESY
121COSY
131TOCSY
1411H-15N HSQC
151HMQC-J
161HSQC-NOESY
171HSQC-TOCSY
NMR detailsText: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS ...Text: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS WERE MEASURED IN A 1H-15N HMQC-J SPECTRUM. SEE REFERENCE 1 FOR DETAILS OF 1JHN CONSTRAINT IMPLEMENTATION.

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Sample preparation

DetailsContents: SEE REFERENCES
Sample conditionsIonic strength: SEE REFERENCES / pH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built6001
GE OMEGAGEOMEGA7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGER STRUCTURAL STATISTICS: FROM EXPERIMENTAL DISTANCE CONSTRAINTS (A) RMS SIGMA DEVIATIONS FROM EXP. RESTRAINTS DEVIATIONS FROM IDEAL GEOMETRYrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN REFERENCE 1.
NMR ensembleConformer selection criteria: NO NOE, 3JHN OR 1JHN CONSTRAINTS VIOLATED BY > 0.5 A, 5 DEGREES OR 2 HERTZ
Conformers calculated total number: 280 / Conformers submitted total number: 20

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