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- PDB-7lyu: Reelin repeat 8 -

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Basic information

Entry
Database: PDB / ID: 7lyu
TitleReelin repeat 8
ComponentsReelin
KeywordsSIGNALING PROTEIN / glycoprotein / secreted protein / egf-like motif
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: 3 Å
AuthorsTurk, L.S. / Comoletti, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1755189 United States
CitationJournal: Biophys.J. / Year: 2022
Title: Structure of Reelin repeat 8 and the adjacent C-terminal region.
Authors: Turk, L.S. / Currie, M.J. / Dobson, R.C.J. / Comoletti, D.
History
DepositionMar 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_keywords.text
Revision 1.2Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Reelin
B: Reelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,94710
Polymers93,4682
Non-polymers3,4798
Water00
1
A: Reelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6365
Polymers46,7341
Non-polymers1,9024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Reelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3125
Polymers46,7341
Non-polymers1,5784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.171, 104.059, 67.615
Angle α, β, γ (deg.)90.000, 104.109, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3054 through 3099 or resid 3104...
d_2ens_1(chain "B" and ((resid 3054 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILELYSA2 - 40
d_12ens_1THRALAA42 - 211
d_13ens_1VALGLYA213 - 239
d_14ens_1SERPROA241 - 314
d_15ens_1ASPLEUA316 - 362
d_21ens_1ILEPHEB2 - 11
d_22ens_1GLULYSB14 - 42
d_23ens_1THRLYSB45 - 153
d_24ens_1GLUALAB158 - 218
d_25ens_1VALGLYB220 - 246
d_26ens_1SERPROB248 - 321
d_27ens_1ASPLEUB323 - 369

NCS oper: (Code: givenMatrix: (-0.999938215944, -0.000139209413459, -0.0111150760615), (-0.0109799352515, 0.168311931275, 0.98567263065), (0.0017335850094, 0.985733774612, -0.168303060792)Vector: 8. ...NCS oper: (Code: given
Matrix: (-0.999938215944, -0.000139209413459, -0.0111150760615), (-0.0109799352515, 0.168311931275, 0.98567263065), (0.0017335850094, 0.985733774612, -0.168303060792)
Vector: 8.63923341159, -8.42383453201, 10.068156922)

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Components

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Protein / Non-polymers , 2 types, 6 molecules AB

#1: Protein Reelin / Reeler protein


Mass: 46733.984 Da / Num. of mol.: 2 / Fragment: Reelin repeat 8 UNP residues 3052 to 3455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln, Rl / Production host: Homo sapiens (human)
References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH 8, 35% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953724 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 3→45.12 Å / Num. obs: 16263 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 64.52 Å2 / CC1/2: 0.985 / Net I/σ(I): 5.5
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2620 / CC1/2: 0.496

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+26 / Resolution: 3→45.12 Å / SU ML: 0.3849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 826 5.09 %
Rwork0.2271 15414 -
obs0.229 16240 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.81 Å2
Refinement stepCycle: LAST / Resolution: 3→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 226 0 5675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535827
X-RAY DIFFRACTIONf_angle_d0.89497962
X-RAY DIFFRACTIONf_chiral_restr0.0619937
X-RAY DIFFRACTIONf_plane_restr0.00561005
X-RAY DIFFRACTIONf_dihedral_angle_d8.3509912
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.789318584788 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.32881270.30992561X-RAY DIFFRACTION99.78
3.19-3.430.32791280.28282569X-RAY DIFFRACTION99.85
3.43-3.780.30021350.24662564X-RAY DIFFRACTION99.93
3.78-4.330.27781570.21362534X-RAY DIFFRACTION99.85
4.33-5.450.23181340.18932574X-RAY DIFFRACTION99.96
5.45-45.120.21741450.21472612X-RAY DIFFRACTION99.89
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)
11.960224561350.2001721068260.9614958520931.29993132802-0.4297500369380.9693042182950.128732411756-0.407399048672-0.193043098090.01676617222010.0576274601340.196611974836-0.0114746984066-0.2474076220880.0002100302399830.315997705766-0.01204606777340.04983778083580.3878032413380.1029452915670.382672789856-20.4352904068-2.9682378628731.4433412931
21.75776901276-0.690244132537-0.6828304180650.657148633937-0.07492430696530.5455883800290.110660242213-0.6382345455240.1160585297490.0729692797623-0.03551901673670.110717691818-0.2671605975610.1141595152390.007912327294660.414747609917-0.05343521094190.04169187675010.536135816671-0.02149197164670.335754182508-11.03097527962.8601396831631.5816932519
30.9292871082350.258979301716-0.4673123048822.400207423230.3012715522821.20635918810.0590620983527-0.2958940211650.005880731637130.246250453199-0.0472266932981-0.4039336213330.08501748763760.215932204223-0.002548160145640.3027119271840.00469632308461-0.1002271972570.275689732721-0.03503418829770.3184931814812.1468454074-3.9241354040726.2951581055
41.25216381612-0.0871044968797-0.1745981703880.7503129853980.2474368609670.09830517638040.4102062802170.1299878580370.1085589633630.0610226126492-0.435131339345-0.439954031194-0.184867057998-0.1585700186640.02080230784310.319130247184-0.04653307964630.04759593994880.5337043691450.03213308691240.37773442214530.797615960226.73363579561.77152568827
50.3858855744790.346366324016-0.03591268043960.5143213649750.2400119349710.4500247255230.1700070518650.111409540183-0.481180077348-0.14036736777-0.124546133847-0.09162864849030.155467312852-0.0562257373171-7.02682682191E-50.3067321555550.03074736356670.02604700764630.3132027638390.04176409572560.38257363342920.807702309915.44368472314.98780374868
61.497927107820.1920528066020.3965292539831.50612832521-1.248905444841.370457618470.2447411988780.6902041111630.216587494244-0.210280034782-0.0530811304264-0.179837777708-0.294376327406-0.05177132171150.006645374664850.310754788335-0.04092015312770.003593681283840.3886039768510.02412706249220.31501746808524.496991327724.9785295343.32990448855
71.080429919730.344495745277-0.09074795653341.424699067070.6447803822391.318754730350.08266727377010.104319774942-0.0494150964247-0.06390523341480.03764457601570.0303592364625-0.191198424732-0.33078661070.03892412755190.306254274530.06972444320750.02638272820210.2204755455690.03009149500360.219135073631-2.3930193539118.51917167982.51314790164
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3053 through 3160 )AA3053 - 31601 - 98
22chain 'A' and (resid 3161 through 3260 )AA3161 - 326099 - 194
33chain 'A' and (resid 3261 through 3430 )AA3261 - 3430195 - 364
44chain 'B' and (resid 3053 through 3126 )BB3053 - 31261 - 67
55chain 'B' and (resid 3127 through 3205 )BB3127 - 320568 - 146
66chain 'B' and (resid 3206 through 3243 )BB3206 - 3243147 - 184
77chain 'B' and (resid 3244 through 3430 )BB3244 - 3430185 - 371

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