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- PDB-3poy: Crystal Structure of the alpha-Neurexin-1 ectodomain, LNS 2-6 -

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Basic information

Entry
Database: PDB / ID: 3poy
TitleCrystal Structure of the alpha-Neurexin-1 ectodomain, LNS 2-6
ComponentsNeurexin-1-alpha
KeywordsCELL ADHESION / LNS / laminin neurexin sex hormone-binding globulin / EGF / epidermal growth factor / synaptic adhesion protein / neuroligin / NLGN / presynaptic / neurexin / NRXN
Function / homology
Function and homology information


neuroligin family protein binding / cell projection / presynaptic membrane / cell adhesion / metal ion binding
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Neurexin-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsMiller, M.T. / Mileni, M. / Comoletti, D. / Stevens, R.C. / Harel, M. / Taylor, P.
CitationJournal: Structure / Year: 2011
Title: The crystal structure of the alpha-neurexin-1 extracellular region reveals a hinge point for mediating synaptic adhesion and function.
Authors: Miller, M.T. / Mileni, M. / Comoletti, D. / Stevens, R.C. / Harel, M. / Taylor, P.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
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 / struct_asym / struct_conn / 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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3593
Polymers112,5921
Non-polymers7672
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.740, 61.240, 155.580
Angle α, β, γ (deg.)90.00, 121.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neurexin-1-alpha


Mass: 112591.992 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 296-1349) / Mutation: Q628E,I1128F, del(395-409,1263-1292)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid: pCDNA 3.1 / Cell line (production host): HEK293S GNT1- / Production host: Homo sapiens (human) / References: UniProt: Q28146
#2: 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
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 9
Details: 12% PEG20000, 100 mM bicine, 1 mM EDTA, 150 mM NaCl , pH 9.0, VAPOR DIFFUSION, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 15, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.02→38.564 Å / Num. all: 32190 / Num. obs: 31504 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 63.4 Å2 / Rsym value: 0.14 / Net I/σ(I): 8.7
Reflection shellResolution: 3.02→3.13 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 3223 / Rsym value: 0.628 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3BOD, 2HOB, 2R16

3bod

2hob

2r16


Resolution: 3.02→38.56 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / SU B: 42.645 / SU ML: 0.355 / Isotropic thermal model: isotropic + tls (7 groups) / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26913 1586 5 %RANDOM
Rwork0.21356 ---
obs0.21642 29917 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.449 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å23.05 Å2
2--1.24 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 3.02→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7791 0 50 33 7874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228009
X-RAY DIFFRACTIONr_bond_other_d00.025368
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.96410853
X-RAY DIFFRACTIONr_angle_other_deg4.2843.00113062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31651002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03824.59366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.235151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028950
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021596
X-RAY DIFFRACTIONr_mcbond_it0.8811.54968
X-RAY DIFFRACTIONr_mcbond_other01.52065
X-RAY DIFFRACTIONr_mcangle_it1.23528001
X-RAY DIFFRACTIONr_scbond_it0.4633041
X-RAY DIFFRACTIONr_scangle_it0.6714.52852
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 107 -
Rwork0.312 2243 -
obs-2243 99.7 %
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)
13.9611-1.18540.31261.37210.68412.29760.0880.06690.1055-0.040.0846-0.02480.04820.0598-0.17260.346-0.0672-0.01780.29790.01410.201785.254527.1343-78.9791
22.7982-1.3425-0.98664.50770.06375.2439-0.07850.2041-0.48340.01650.0790.34670.4725-0.3525-0.00050.2461-0.08140.06670.28530.01270.178468.670825.4983-52.149
34.51272.0301-10.00294.2774-3.84721.89380.54820.13670.26820.1221-0.0998-0.5333-1.2350.0879-0.44840.48630.10080.15030.33820.19230.43461.324747.4434-36.7456
42.96070.5628-1.03412.1654-0.31424.8076-0.07250.1162-0.0467-0.25080.0192-0.15270.04920.09280.05340.05460.01070.03490.01020.00550.087860.497526.9425-21.0676
52.68860.69370.90964.7009-0.10392.55830.0175-0.1148-0.30730.2105-0.0549-0.22810.14520.17850.03730.0562-0.00320.02720.02320.0150.068258.854131.71939.7583
610.57494.21713.31475.84024.54874.87430.4295-0.82250.50540.1704-0.59230.0811-0.4147-1.01890.16280.2260.18690.00130.31960.00520.22422.088921.6427-3.1178
74.7905-1.2920.21644.48860.19634.25730.11650.0983-0.3695-0.298-0.00130.2198-0.025-0.6922-0.11510.0665-0.0108-0.05120.34390.00770.21037.937810.1221-20.3948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A278 - 460
2X-RAY DIFFRACTION2A473 - 665
3X-RAY DIFFRACTION3A668 - 705
4X-RAY DIFFRACTION4A706 - 895
5X-RAY DIFFRACTION5A896 - 1074
6X-RAY DIFFRACTION6A1075 - 1112
7X-RAY DIFFRACTION7A1115 - 1291

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