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- PDB-5b4y: Crystal structure of the LA12 fragment of ApoER2 -

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Basic information

Entry
Database: PDB / ID: 5b4y
TitleCrystal structure of the LA12 fragment of ApoER2
ComponentsLow-density lipoprotein receptor-related protein 8
KeywordsSIGNALING PROTEIN / signal transduction
Function / homology
Function and homology information


ammon gyrus development / reelin receptor activity / positive regulation of CREB transcription factor activity / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / reelin-mediated signaling pathway / high-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / layer formation in cerebral cortex / positive regulation of dendritic spine morphogenesis ...ammon gyrus development / reelin receptor activity / positive regulation of CREB transcription factor activity / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / reelin-mediated signaling pathway / high-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / layer formation in cerebral cortex / positive regulation of dendritic spine morphogenesis / cellular response to cholesterol / positive regulation of dendrite development / dendrite morphogenesis / cargo receptor activity / microtubule associated complex / retinoid metabolic process / regulation of innate immune response / Platelet sensitization by LDL / apolipoprotein binding / kinesin binding / positive regulation of protein tyrosine kinase activity / Retinoid metabolism and transport / caveola / modulation of chemical synaptic transmission / lipid metabolic process / cellular response to growth factor stimulus / endocytosis / cytokine-mediated signaling pathway / calcium-dependent protein binding / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / amyloid-beta binding / chemical synaptic transmission / regulation of apoptotic process / receptor complex / response to xenobiotic stimulus / axon / dendrite / neuronal cell body / synapse / calcium ion binding / cell surface / signal transduction / proteolysis / extracellular space / 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 / 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 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. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNogi, T. / Tabata, S. / Hirai, H. / Yasui, N. / Takagi, J.
CitationJournal: To Be Published
Title: Crystal structure of the ectodomain from a LDLR close homologue in complex with its physiological ligand.
Authors: Hirai, H. / Yasui, N. / Yamashita, K. / Tabata, S. / Yamamoto, M. / Takagi, J. / Nogi, T.
History
DepositionApr 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Low-density lipoprotein receptor-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7043
Polymers9,6241
Non-polymers802
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.162, 41.780, 55.063
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 Low-density lipoprotein receptor-related protein 8 / LRP-8 / Apolipoprotein E receptor 2


Mass: 9624.260 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP8, APOER2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14114
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP Q14114 shows Natural variant at this position

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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: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20%(wt./vol.) PEG monomethylether 2000, 100 mM Tris-Cl (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→41.8 Å / Num. obs: 6043 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→1.94 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7Q

3a7q


Resolution: 1.9→33.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.523 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24667 302 5 %RANDOM
Rwork0.21023 ---
obs0.21197 5710 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.362 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--2.18 Å20 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.9→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 2 35 663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.929880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98126.42942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.663154
X-RAY DIFFRACTIONr_chiral_restr0.1260.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 32 -
Rwork0.315 390 -
obs--100 %

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