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- PDB-2e26: Crystal structure of two repeat fragment of reelin -

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Entry
Database: PDB / ID: 2.0E+26
TitleCrystal structure of two repeat fragment of reelin
ComponentsReelin
KeywordsSIGNALING PROTEIN
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 / Galactose-binding domain-like ...: / Reelin subrepeat B / Reelin / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Reelin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYasui, N. / Nogi, T. / Kitao, T. / Takagi, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of a receptor-binding fragment of reelin and mutational analysis reveal a recognition mechanism similar to endocytic receptors.
Authors: Yasui, N. / Nogi, T. / Kitao, T. / Nakano, Y. / Hattori, M. / Takagi, J.
History
DepositionNov 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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_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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,15312
Polymers81,3491
Non-polymers1,80411
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.008, 70.953, 94.769
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reelin / Reeler protein


Mass: 81349.148 Da / Num. of mol.: 1 / Fragment: residues 1948-2661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln, Rl / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1
References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 2
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 , 4 types, 506 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7% PEG 3350, 75mM ammonium acetate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→94.491 Å / Num. all: 77500 / Num. obs: 54041 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 3.5 / Num. unique all: 51309 / % possible all: 98.73

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DDU

2ddu


Resolution: 2→47.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.879 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21884 2732 5.1 %RANDOM
Rwork0.17923 ---
all0.21884 ---
obs0.18125 51309 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.264 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å21.47 Å2
2--0.19 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 105 499 6154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.967998
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11123.764271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20815898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1351535
X-RAY DIFFRACTIONr_chiral_restr0.0760.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024504
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24005
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921.53636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98425699
X-RAY DIFFRACTIONr_scbond_it1.44232587
X-RAY DIFFRACTIONr_scangle_it2.3114.52291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 164 -
Rwork0.194 3380 -
obs--88.01 %
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)
11.3099-0.0205-0.50341.8094-0.04091.6324-0.02550.0587-0.0292-0.1983-0.0057-0.05210.07130.00120.0312-0.04420.00580.0205-0.10330.0207-0.048443.4013-3.369-17.3907
27.29015.3432-8.06024.6808-3.781214.8266-0.21640.8750.1882-0.36830.49820.45530.3873-1.6291-0.2818-0.1121-0.0376-0.07210.12680.0691-0.100721.3627-3.7618-20.6348
31.9741-0.04-0.16341.1506-0.46692.3375-0.043-0.0433-0.0132-0.01190.0298-0.05250.014-0.00430.0132-0.0691-0.0149-0.0102-0.0956-0.0066-0.053428.6650.70165.2419
41.08980.0232-0.52281.0566-0.17812.25350.0102-0.09190.03150.11960.0281-0.0042-0.0362-0.0211-0.0383-0.08660.0115-0.0161-0.0344-0.0034-0.04997.8358-2.584524.7484
56.10531.0026-1.16432.73481.02457.1969-0.0354-0.1609-0.13330.049-0.03380.04810.5188-0.42360.0692-0.1165-0.0189-0.02240.0720.0278-0.0756-14.2644-6.93924.0582
62.29490.1441-0.8911.02120.15554.52660.07690.07880.08790.0619-0.00860.0576-0.2816-0.1764-0.0683-0.01560.04480.0686-0.11490.0044-0.118-7.6841.785148.3003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1956 - 213111 - 186
2X-RAY DIFFRACTION2AA2132 - 2166187 - 221
3X-RAY DIFFRACTION3AA2167 - 2319222 - 374
4X-RAY DIFFRACTION4AA2320 - 2481375 - 536
5X-RAY DIFFRACTION5AA2482 - 2515537 - 570
6X-RAY DIFFRACTION6AA2516 - 2663571 - 718

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