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- PDB-1j8e: Crystal structure of ligand-binding repeat CR7 from LRP -

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Basic information

Entry
Database: PDB / ID: 1j8e
TitleCrystal structure of ligand-binding repeat CR7 from LRP
ComponentsLOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1
KeywordsSIGNALING PROTEIN / ligand binding / calcium binding / complement-like repeat / LRP receptor
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis / negative regulation of smooth muscle cell migration / regulation of cholesterol transport / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / regulation of extracellular matrix disassembly / amyloid-beta clearance by cellular catabolic process / scavenger receptor activity / plasma membrane protein complex / positive regulation of amyloid-beta clearance / transcytosis / heparan sulfate proteoglycan binding / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / lysosomal transport / retinoid metabolic process / microtubule organizing center / lipoprotein transport / negative regulation of SMAD protein signal transduction / enzyme-linked receptor protein signaling pathway / negative regulation of Wnt signaling pathway / amyloid-beta clearance / positive regulation of endocytosis / apolipoprotein binding / transport across blood-brain barrier / positive regulation of cholesterol efflux / Scavenging of heme from plasma / phagocytosis / clathrin-coated pit / Retinoid metabolism and transport / receptor-mediated endocytosis / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / lipid metabolic process / receptor internalization / cellular response to amyloid-beta / endocytic vesicle membrane / positive regulation of protein binding / signaling receptor activity / amyloid-beta binding / basolateral plasma membrane / early endosome / receptor complex / lysosomal membrane / negative regulation of gene expression / focal adhesion / calcium ion binding / protein-containing complex binding / Golgi apparatus / RNA binding / membrane / nucleus / plasma membrane
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Complement Clr-like EGF domain / 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 ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Complement Clr-like EGF domain / 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. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / 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 signature 1. / EGF-like domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSimonovic, M. / Dolmer, K. / Huang, W. / Strickland, D.K. / Volz, K. / Gettins, P.G.W.
CitationJournal: Biochemistry / Year: 2001
Title: Calcium coordination and pH dependence of the calcium affinity of ligand-binding repeat CR7 from the LRP. Comparison with related domains from the LRP and the LDL receptor.
Authors: Simonovic, M. / Dolmer, K. / Huang, W. / Strickland, D.K. / Volz, K. / Gettins, P.G.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8171
Non-polymers401
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.588, 35.359, 36.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1


Mass: 4817.019 Da / Num. of mol.: 1
Fragment: COMPLEMENT-LIKE REPEAT 7 (CR7), LDL-RECEPTOR CLASS A 7
Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07954
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 1.84 Å3/Da / Density % sol: 33.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.02M Na-acetate, 0.1M CaCl2, 0.3M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
20.3 M1reservoirNaCl
320 mMsodium acetate1reservoirpH3.8
4100 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 86028 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.268 / Num. unique all: 274 / % possible all: 56.6
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 2911 / Num. measured all: 86028
Reflection shell
*PLUS
% possible obs: 56.6 % / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Composite search model constructed based on coordinates of 1AJJ, 1D2L, and 1CR8.

1ajj

1d2l

1cr8


Resolution: 1.85→21.96 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1341106.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 281 9.7 %RANDOM
Rwork0.186 ---
obs-2911 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.37 Å2 / ksol: 0.419 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2---6.09 Å20 Å2
3---3.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms332 0 1 31 364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 28 9.3 %
Rwork0.227 274 -
obs-274 56.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.PARAM
X-RAY DIFFRACTION3ION.PARAMWATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 21.96 Å / σ(F): 0 / % reflection Rfree: 9.7 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.227

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