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- PDB-6a48: Crystal structure of reelin N-terminal region -

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Basic information

Entry
Database: PDB / ID: 6a48
TitleCrystal structure of reelin N-terminal region
ComponentsReelin
KeywordsSIGNALING PROTEIN / Reelin / extracellular protein / LDLR family
Function / homology
Function and homology information


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 / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering ...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 / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering / positive regulation of CREB transcription factor activity / postsynaptic density assembly / ventral spinal cord development / reelin-mediated signaling pathway / regulation of behavior / positive regulation of synapse maturation / motor neuron migration / regulation of neuron migration / layer formation in cerebral cortex / glial cell differentiation / receptor localization to synapse / positive regulation of dendritic spine morphogenesis / protein localization to synapse / NMDA glutamate receptor clustering / very-low-density lipoprotein particle receptor binding / dentate gyrus development / positive regulation of small GTPase mediated signal transduction / regulation of NMDA receptor activity / positive regulation of AMPA receptor activity / regulation of neuron differentiation / response to pain / dendrite development / associative learning / positive regulation of excitatory postsynaptic potential / positive regulation of protein tyrosine kinase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / long-term memory / forebrain development / serine-type peptidase activity / positive regulation of synaptic transmission, glutamatergic / extracellular matrix / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / hippocampus development / long-term synaptic potentiation / axon guidance / neuron migration / modulation of chemical synaptic transmission / cell morphogenesis / brain development / cerebral cortex development / positive regulation of neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / regulation of gene expression / perikaryon / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / neuron projection / positive regulation of protein phosphorylation / axon / neuronal cell body / dendrite / proteolysis / extracellular space / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Reelin subrepeat B / Reelin / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. ...: / Reelin subrepeat B / Reelin / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNagae, M. / Takagi, J.
CitationJournal: J.Biochem. / Year: 2021
Title: Structural studies of reelin N-terminal region provides insights into a unique structural arrangement and functional multimerization.
Authors: Nagae, M. / Suzuki, K. / Yasui, N. / Nogi, T. / Kohno, T. / Hattori, M. / Takagi, J.
History
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 29, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8459
Polymers75,9811
Non-polymers8648
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-5 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.753, 90.999, 90.535
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 Reelin / Reeler protein


Mass: 75980.852 Da / Num. of mol.: 1 / Fragment: N-terminal region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln, Rl / Plasmid: pcDNA3.1-His/Myc / Cell line (production host): CHO 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl (pH 8.0), 0.4M sodium chloride,25% (w/v) PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 46788 / % possible obs: 97.2 % / Redundancy: 6.4 % / Rsym value: 0.099 / Net I/σ(I): 26
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4744 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+26 / Resolution: 2→45.267 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2569 2363 5.07 %
Rwork0.2146 --
obs0.2168 46572 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 47 151 5330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055324
X-RAY DIFFRACTIONf_angle_d0.8177249
X-RAY DIFFRACTIONf_dihedral_angle_d14.1193126
X-RAY DIFFRACTIONf_chiral_restr0.064785
X-RAY DIFFRACTIONf_plane_restr0.004936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.33751290.29252610X-RAY DIFFRACTION99
2.0408-2.08520.30721310.29072604X-RAY DIFFRACTION99
2.0852-2.13370.29021410.26552645X-RAY DIFFRACTION99
2.1337-2.18710.29811260.2562613X-RAY DIFFRACTION99
2.1871-2.24620.34631520.25472586X-RAY DIFFRACTION98
2.2462-2.31230.28751430.25292586X-RAY DIFFRACTION97
2.3123-2.38690.30581420.24732593X-RAY DIFFRACTION98
2.3869-2.47220.3091520.24912572X-RAY DIFFRACTION97
2.4722-2.57120.30721380.24292567X-RAY DIFFRACTION97
2.5712-2.68820.28821300.24122565X-RAY DIFFRACTION96
2.6882-2.82990.26761240.23842567X-RAY DIFFRACTION95
2.8299-3.00720.30591330.24942529X-RAY DIFFRACTION95
3.0072-3.23930.27611350.23772520X-RAY DIFFRACTION94
3.2393-3.56520.26131330.20482526X-RAY DIFFRACTION93
3.5652-4.08080.22871420.18062559X-RAY DIFFRACTION95
4.0808-5.14020.17821570.14992706X-RAY DIFFRACTION99
5.1402-45.27910.22581550.19422861X-RAY DIFFRACTION100

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