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- PDB-3a7q: Structural basis for specific recognition of reelin by its receptors -

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Basic information

Entry
Database: PDB / ID: 3a7q
TitleStructural basis for specific recognition of reelin by its receptors
Components
  • Low-density lipoprotein receptor-related protein 8
  • Reelin
KeywordsSIGNALING PROTEIN
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 / 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 / extracellular space
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 / Reelin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYasui, N. / Nogi, T. / Takagi, J.
CitationJournal: Structure / Year: 2010
Title: Structural Basis for Specific Recognition of Reelin by Its Receptors
Authors: Yasui, N. / Nogi, T. / Takagi, J.
History
DepositionOct 1, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,75312
Polymers86,4002
Non-polymers1,35410
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Reelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63110
Polymers81,3171
Non-polymers1,3149
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Low-density lipoprotein receptor-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1232
Polymers5,0821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.980, 93.844, 73.456
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Reelin / Reeler protein


Mass: 81317.078 Da / Num. of mol.: 1 / Fragment: repeat 5-6 fragment, UNP residues 1948-2661 / Mutation: C2101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln / Plasmid: pcDNA3.1 / Cell line (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): lec 3.2.8.1 / Tissue (production host): ovary
References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Low-density lipoprotein receptor-related protein 8 / Apolipoprotein E receptor 2


Mass: 5082.448 Da / Num. of mol.: 1 / Fragment: LA1 module, UNP residues 42-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOER2 / Plasmid: pGEX-3T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q14114

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 3
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

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Non-polymers , 3 types, 25 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1, 2, 3, 5 AND 12 IN THE DATABASE UNIPROTKB/SWISS-PROT Q14114 ...THE SEQUENCE IS BASED ON REFERENCE 1, 2, 3, 5 AND 12 IN THE DATABASE UNIPROTKB/SWISS-PROT Q14114 (LRP8_HUMAN). D46E IS NATURAL VARIENT OF LRP8_HUMAN.

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 36-38% MPD, 21-25% PEG 1000, 100mM HEPES-Na pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→46.93 Å / Num. obs: 21990 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3213 / Rsym value: 0.374 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E26

2e26


Resolution: 2.6→46.93 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.866 / SU B: 30.323 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29603 1135 5.2 %RANDOM
Rwork0.22324 ---
obs0.22695 20837 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.776 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å2-4.93 Å2
2---1.77 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 76 19 5791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215974
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.958116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9823.875289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1511538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024612
X-RAY DIFFRACTIONr_nbd_refined0.2070.22471
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2227
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.27
X-RAY DIFFRACTIONr_mcbond_it0.3781.53697
X-RAY DIFFRACTIONr_mcangle_it0.64225784
X-RAY DIFFRACTIONr_scbond_it0.92732634
X-RAY DIFFRACTIONr_scangle_it1.4594.52332
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 87 -
Rwork0.255 1554 -
obs--99.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5497-0.2881.84246.3559-0.16623.4678-0.1098-0.24660.081-0.0028-0.0588-0.0583-0.10830.01530.1686-0.2733-0.01550.0519-0.168-0.0089-0.319-20.8971-2.42115.5661
212.0174-2.25159.77690.4218-1.827112.4298-1.361-1.09491.54490.23010.1071-0.0005-0.71730.00731.25390.25940.0568-0.2194-0.0115-0.24790.2722-16.130216.298916.4798
36.1253-2.04711.80765.44481.88744.91030.30120.1522-0.775-0.1278-0.13140.23650.19720.1189-0.1699-0.1638-0.0186-0.0623-0.14940.0247-0.07916.0161-1.484316.7991
41.88910.78910.67434.3154-1.31233.6962-0.14390.1682-0.0692-0.11080.1401-0.25910.11810.25650.0037-0.1513-0.0050.0569-0.0523-0.0026-0.245724.70282.83239.2105
518.57472.43513.43724.11134.492416.0162-0.258-0.81840.80810.1376-0.03850.1684-0.47-0.26090.2965-0.06910.07790.08540.0057-0.0102-0.141926.579518.229855.2556
64.2941-2.53321.23995.28030.81472.6328-0.01480.0050.09960.11370.131-0.41090.06980.0227-0.1162-0.1891-0.0140.0381-0.1482-0.0083-0.224948.46292.687153.2275
73.0956-2.2281-2.771813.0205-6.5088.8147-0.5985-0.1761-0.80780.46430.30751.4342-0.0553-0.24750.2910.14120.00060.0394-0.0349-0.06620.094815.1376-21.130252.1721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1953 - 2131
2X-RAY DIFFRACTION1A4001
3X-RAY DIFFRACTION2A2132 - 2165
4X-RAY DIFFRACTION2A3001
5X-RAY DIFFRACTION3A2166 - 2319
6X-RAY DIFFRACTION3A4002
7X-RAY DIFFRACTION3A3002 - 3004
8X-RAY DIFFRACTION3A6001
9X-RAY DIFFRACTION4A2320 - 2480
10X-RAY DIFFRACTION4A4003
11X-RAY DIFFRACTION4A4005
12X-RAY DIFFRACTION4A6002
13X-RAY DIFFRACTION5A2481 - 2515
14X-RAY DIFFRACTION6A2516 - 2662
15X-RAY DIFFRACTION6A4004
16X-RAY DIFFRACTION6A3005
17X-RAY DIFFRACTION6A6003
18X-RAY DIFFRACTION7B47 - 81
19X-RAY DIFFRACTION7B5001

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