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- PDB-2lgp: Solution structure of LA45 from LDLR -

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Basic information

Entry
Database: PDB / ID: 2lgp
TitleSolution structure of LA45 from LDLR
ComponentsLow-density lipoprotein receptor
KeywordsPROTEIN BINDING / complement repeat
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 / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 2
AuthorsGuttman, M. / Komives, E.A.
CitationJournal: Biochemistry / Year: 2011
Title: The Structure, Dynamics, and Binding of the LA45 Module Pair of the Low-Density Lipoprotein Receptor Suggest an Important Role for LA4 in Ligand Release.
Authors: Guttman, M. / Komives, E.A.
History
DepositionAug 1, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2493
Polymers10,1691
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 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 10169.036 Da / Num. of mol.: 1
Fragment: LDL-receptor class A 4 and A5 domain residues 144-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: CELL-FREE SYNTHESIS (others) / 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 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D 1H-1H COSY
1922D 1H-1H COSY
11022D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 20 mM [U-99% 2H] HEPES, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1-1[U-99% 13C; U-99% 15N]1
5 mMCALCIUM ION-21
0.02 %sodium azide-31
20 mMHEPES-4[U-99% 2H]1
150 mMsodium chloride-51
0.8 mMentity_1-6[U-99% 13C; U-99% 15N]2
5 mMCALCIUM ION-72
0.02 %sodium azide-82
150 mMsodium chloride-92
20 mMHEPES-10[U-99% 2H]2
Sample conditionsIonic strength: 0.15 / pH: 7.45 / Pressure: ambient / Temperature: 306 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AzaraBoucherprocessing
ARIA2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2Linge, O'Donoghue and Nilgesdata analysis
ARIA2Linge, O'Donoghue and Nilgesrefinement
CNSSOLVE2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSSOLVE2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2453 / NOE intraresidue total count: 389 / NOE long range total count: 538 / NOE medium range total count: 424 / NOE sequential total count: 499 / Hydrogen bond constraints total count: 12 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 25
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.0414 Å / Distance rms dev error: 0.00359 Å

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