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- PDB-5b4x: Crystal structure of the ApoER2 ectodomain in complex with the Re... -

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Basic information

Entry
Database: PDB / ID: 5b4x
TitleCrystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment
Components
  • Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
  • Reelin
KeywordsSIGNALING PROTEIN/ENDOCYTOSIS / signal transduction / MEMBRANE PROTEIN / SIGNALING PROTEIN-ENDOCYTOSIS complex
Function / homology
Function and homology information


ammon gyrus development / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / Reelin signalling pathway / lipoprotein particle receptor binding / positive regulation of AMPA receptor activity / regulation of synaptic activity ...ammon gyrus development / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / Reelin signalling pathway / lipoprotein particle receptor binding / positive regulation of AMPA receptor activity / regulation of synaptic activity / interneuron migration / positive regulation of CREB transcription factor activity / postsynaptic density protein 95 clustering / postsynaptic density assembly / reelin receptor activity / regulation of behavior / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / positive regulation of synapse maturation / high-density lipoprotein particle binding / layer formation in cerebral cortex / motor neuron migration / receptor localization to synapse / low-density lipoprotein particle receptor activity / NMDA glutamate receptor clustering / glial cell differentiation / regulation of neuron migration / positive regulation of dendritic spine morphogenesis / cellular response to cholesterol / protein localization to synapse / reelin-mediated signaling pathway / very-low-density lipoprotein particle receptor binding / regulation of synapse maturation / regulation of NMDA receptor activity / positive regulation of small GTPase mediated signal transduction / cargo receptor activity / microtubule associated complex / regulation of neuron differentiation / positive regulation of dendrite development / dendrite morphogenesis / response to pain / Platelet sensitization by LDL / regulation of innate immune response / positive regulation of protein tyrosine kinase activity / associative learning / dendrite development / kinesin binding / apolipoprotein binding / positive regulation of excitatory postsynaptic potential / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / long-term memory / membrane => GO:0016020 / retinoid metabolic process / Retinoid metabolism and transport / forebrain development / serine-type peptidase activity / extracellular matrix / positive regulation of synaptic transmission, glutamatergic / axon guidance / hippocampus development / central nervous system development / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / modulation of chemical synaptic transmission / postsynaptic density membrane / cytokine-mediated signaling pathway / brain development / cell morphogenesis / cellular response to growth factor stimulus / Schaffer collateral - CA1 synapse / cerebral cortex development / positive regulation of neuron projection development / caveola / lipid metabolic process / long-term synaptic potentiation / endocytosis / neuron migration / calcium-dependent protein binding / transmembrane signaling receptor activity / cell migration / amyloid-beta binding / regulation of gene expression / : / regulation of apoptotic process / chemical synaptic transmission / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / receptor ligand activity / response to xenobiotic stimulus / axon / neuronal cell body / dendrite / calcium ion binding / glutamatergic synapse / cell surface / signal transduction / proteolysis
Similarity search - Function
Reelin / : / Reelin subrepeat B / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Teneurin-like EGF domain / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. ...Reelin / : / Reelin subrepeat B / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Teneurin-like EGF domain / : / 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 / Sialidase superfamily / Galactose-binding domain-like / 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 1. / EGF-like domain signature 2. / EGF-like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e / Low-density lipoprotein receptor-related protein 8 / Reelin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsYasui, N. / Hirai, H. / Yamashita, K. / Takagi, J. / Nogi, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS22247010 Japan
JSPS20770084 Japan
JSPS05J09821 Japan
MEXT17082004 Japan
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: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reelin
B: Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
C: Reelin
D: Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,61825
Polymers290,8704
Non-polymers1,74721
Water00
1
A: Reelin
B: Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,41913
Polymers145,4352
Non-polymers98411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-61 kcal/mol
Surface area55860 Å2
MethodPISA
2
C: Reelin
D: Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,19812
Polymers145,4352
Non-polymers76310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-28 kcal/mol
Surface area56600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.951, 205.951, 169.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Reelin / Reeler protein


Mass: 81786.039 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1948-2662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln, Rl / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e / LRP-8 / Apolipoprotein E receptor 2


Mass: 63649.109 Da / Num. of mol.: 2 / Fragment: ApoER2 ectodomain (UNP RESIDUES 42-607)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP8, hCG_33395 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: D3DQ39, UniProt: Q14114*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 3.59 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11-12.5%(wt./vol.) PEG 3350 200-250mM sodium thiocyanate, 20mM HEPES-Na (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 3.2→49.52 Å / Num. obs: 67441 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Net I/σ(I): 16.4
Reflection shellResolution: 3.2→3.28 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→49.52 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.108 / SU ML: 0.342 / Cross valid method: FREE R-VALUE / ESU R Free: 0.451
RfactorNum. reflection% reflectionSelection details
Rfree0.25481 3467 5.1 %RANDOM
Rwork0.19999 ---
obs0.20277 63926 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 99.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å22.07 Å20 Å2
2--2.07 Å20 Å2
3----6.7 Å2
Refinement stepCycle: 1 / Resolution: 3.2→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18806 0 86 0 18892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01919507
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9526425
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94252369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44624.159945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.674153055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21515120
X-RAY DIFFRACTIONr_chiral_restr0.0820.22809
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115046
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: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 261 -
Rwork0.26 4736 -
obs--100 %

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