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- PDB-1ajj: LDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING -

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Basic information

Entry
Database: PDB / ID: 1ajj
TitleLDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING
ComponentsLOW-DENSITY LIPOPROTEIN RECEPTOR
KeywordsRECEPTOR / LDL RECEPTOR / CYSTEINE-RICH MODULE / CALCIUM
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 / response to caloric restriction / 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 / cellular response to fatty acid / negative regulation of amyloid fibril formation / 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 / positive regulation of inflammatory response / 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 / 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
: / 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. ...: / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsFass, D. / Blacklow, S.C. / Kim, P.S. / Berger, J.M.
Citation
Journal: Nature / Year: 1997
Title: Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module.
Authors: Fass, D. / Blacklow, S. / Kim, P.S. / Berger, J.M.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Protein Folding and Calcium Binding Defects Arising from Familial Hypercholesterolemia Mutations of the Ldl Receptor
Authors: Blacklow, S.C. / Kim, P.S.
History
DepositionMay 4, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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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)4,2063
Polymers4,0691
Non-polymers1362
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.450, 53.450, 26.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide LOW-DENSITY LIPOPROTEIN RECEPTOR / LR5


Mass: 4069.431 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, FIFTH REPEAT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PMM-LR5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01130
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 28 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, PH 5.0, 25% SUCROSE
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
25 mM1dropCaCl2
32.1 Mammonium sulfate1reservoirpH5.0
425 %sucrose1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 2959 / % possible obs: 94.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rsym value: 0.054 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 7 / Rsym value: 0.169 / % possible all: 87.7
Reflection
*PLUS
Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 227 7.7 %RANDOM
Rwork0.209 ---
obs0.209 2959 94.3 %-
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms279 0 6 30 315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.498
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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