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- PDB-3qcw: Structure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts -

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Basic information

Entry
Database: PDB / ID: 3qcw
TitleStructure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts
ComponentsNeurexin-1-alpha
KeywordsCELL ADHESION / synaptic adhesion molecule
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-type aspartate/asparagine hydroxylation site / EGF-like domain ...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-type aspartate/asparagine hydroxylation site / EGF-like domain / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 2.65 Å
AuthorsRudenko, G.
CitationJournal: Structure / Year: 2011
Title: The Structure of Neurexin 1 alpha Reveals Features Promoting a Role as Synaptic Organizer
Authors: Chen, F. / Venugopal, V. / Murray, B. / Rudenko, G.
History
DepositionJan 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurexin-1-alpha
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,7984
Polymers274,9492
Non-polymers8492
Water0
1
A: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8992
Polymers137,4751
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8992
Polymers137,4751
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.953, 114.543, 159.581
Angle α, β, γ (deg.)90.610, 90.870, 92.180
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A281 - 485
2111B281 - 485
1121A486 - 679
2121B486 - 679
1131A680 - 722
2131B680 - 722
1141A723 - 909
2141B723 - 909
1151A910 - 1087
2151B910 - 1087
1161A1088 - 1130
2161B1088 - 1130
1171A1131 - 2001
2171B1131 - 2001

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein Neurexin-1-alpha


Mass: 137474.641 Da / Num. of mol.: 2 / Fragment: UNP residues 31-1355 / Mutation: N190Q, SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q28146
#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.: 2
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
Sequence detailsPROTEIN CONSTRUCT IS A SPLICE FORM THAT DOES NOT CONTAIN SPLICE INSERTS AT SITES SS1 [DEL(258-277)] ...PROTEIN CONSTRUCT IS A SPLICE FORM THAT DOES NOT CONTAIN SPLICE INSERTS AT SITES SS1 [DEL(258-277)], SS2 [DEL(378-393)], SS3 [DEL(790-799),D790G], AND SS4 [DEL(1248-1278)]. Q612E AND I1112F ARE NATURAL ISOFORMS.

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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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5-10% PEG8000 or PEG10000, 2.5 mM calcium chloride, 100 mM bicine, pH 8.0-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 17.83 / Number: 267276 / Rmerge(I) obs: 0.135 / Χ2: 1.9 / D res high: 3.25 Å / D res low: 50 Å / Num. obs: 67601 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.815096.210.0354.0143.9
78.8198.310.0512.7894
6.11798.810.0742.3134
5.566.1198.710.0831.9954
5.165.5698.710.0882.1584
4.855.169910.0942.0474
4.614.859910.0912.0084
4.414.6198.610.1071.964
4.244.4199.210.131.8244
4.094.2498.710.1741.7154
3.974.0999.210.1821.6854
3.853.9798.810.2181.5824
3.753.8599.110.261.5794
3.663.7598.810.3071.5294
3.583.6698.910.361.5544
3.53.5898.710.3881.5114
3.433.598.810.4871.4743.9
3.373.4398.910.5581.4383.9
3.313.3798.410.6341.3943.8
3.253.3197.910.8021.4533.7
ReflectionResolution: 2.65→50 Å / Num. obs: 124701 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Χ2: 1.591 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.73.20.52662061.239198.2
2.7-2.743.30.4561691.203197.7
2.74-2.83.30.42461871.306197.3
2.8-2.853.30.3862111.331198.4
2.85-2.923.30.32161911.33196.9
2.92-2.983.30.25262221.39199.2
2.98-3.063.40.21562001.479197
3.06-3.143.40.18262401.575199.4
3.14-3.233.40.14661871.441197.5
3.23-3.343.40.1362511.544199.3
3.34-3.463.40.11162261.687198.3
3.46-3.63.40.09262911.75198
3.6-3.763.40.08262041.814199.6
3.76-3.963.40.07662781.93198.8
3.96-4.213.40.06662311.958198.7
4.21-4.533.40.0662911.954199.1
4.53-4.993.40.05363121.948199.1
4.99-5.713.40.05262671.822199.1
5.71-7.193.40.04862981.615199.5
7.19-503.30.03662391.398198.6

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2745 / WRfactor Rwork: 0.2672 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8568 / SU B: 16.733 / SU ML: 0.161 / SU R Cruickshank DPI: 0.3693 / SU Rfree: 0.2628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 6451 5.2 %RANDOM
Rwork0.2082 ---
obs0.2093 116726 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 200.33 Å2 / Biso mean: 65.5416 Å2 / Biso min: 2.83 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å2-1.23 Å20.31 Å2
2--0.45 Å20.16 Å2
3---3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15384 0 56 0 15440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215772
X-RAY DIFFRACTIONr_angle_refined_deg1.731.95521400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.89452004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06524.52708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.218152590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4741584
X-RAY DIFFRACTIONr_chiral_restr0.1070.22398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211978
X-RAY DIFFRACTIONr_nbd_refined0.2320.26371
X-RAY DIFFRACTIONr_nbtor_refined0.3210.210789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.216
X-RAY DIFFRACTIONr_mcbond_it0.7431.510119
X-RAY DIFFRACTIONr_mcangle_it1.222215916
X-RAY DIFFRACTIONr_scbond_it2.18136339
X-RAY DIFFRACTIONr_scangle_it3.3174.55484
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11409TIGHT POSITIONAL0.020.05
11409TIGHT THERMAL0.030.5
21510TIGHT POSITIONAL0.030.05
21510TIGHT THERMAL0.050.5
3330TIGHT POSITIONAL0.030.05
3330TIGHT THERMAL0.070.5
41408TIGHT POSITIONAL0.040.05
41408TIGHT THERMAL0.120.5
51374TIGHT POSITIONAL0.040.05
51374TIGHT THERMAL0.130.5
6305TIGHT POSITIONAL0.030.05
6305TIGHT THERMAL0.080.5
71384TIGHT POSITIONAL0.030.05
71384TIGHT THERMAL0.080.5
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 491 -
Rwork0.307 8443 -
all-8934 -
obs--97.78 %
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)
17.59444.32072.18628.35752.95824.8790.05320.02820.7198-0.3264-0.56540.1641-0.86360.05610.51220.6984-0.0409-0.05731.15560.1854-0.07241.4872127.147619.2269
21.39860.1905-0.18580.96050.05393.9436-0.07790.98540.1288-0.59230.0588-0.0044-0.37820.00620.0192-0.0254-0.0546-0.02140.2240.0238-0.3086.011119.48466.0445
34.1354-0.207-0.38362.9049-0.47641.4697-0.00380.05-0.4686-0.00330.02710.2510.1491-0.1926-0.0234-0.43030.0046-0.0027-0.45790.0244-0.32089.780499.9776108.0571
43.221-1.03890.83265.5214-0.01742.2056-0.072-0.1380.75630.19370.10670.0952-0.69390.0447-0.03470.0168-0.04830.078-0.4046-0.06360.256-10.8344154.7958110.5526
59.4967-4.3123-1.76197.69332.55266.008-0.1349-0.1427-0.87760.3539-0.31390.14661.07880.11890.44880.73470.04340.02611.02540.1826-0.071333.6869-16.0905190.715
61.548-0.18110.13481.02260.20743.9861-0.0724-1.01-0.12430.620.0765-0.04080.42850.0299-0.0041-0.02560.0661-0.010.18670.028-0.306739.86-8.7111143.716
74.3740.21270.44113.0854-0.73731.3693-0.0010.01340.4532-0.01480.05980.268-0.1723-0.1965-0.0588-0.4202-0.01070.0019-0.45050.0323-0.309644.673810.5807101.6104
84.96972.6663-1.38295.4781-0.25412.6133-0.27040.1234-1.1714-0.28770.1526-0.37910.81150.13260.11780.06190.06910.0184-0.371-0.07970.365123.8057-44.301599.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A281 - 485
2X-RAY DIFFRACTION2A486 - 909
3X-RAY DIFFRACTION3A910 - 1087
4X-RAY DIFFRACTION4A1088 - 1337
5X-RAY DIFFRACTION5B281 - 485
6X-RAY DIFFRACTION6B486 - 909
7X-RAY DIFFRACTION7B910 - 1087
8X-RAY DIFFRACTION8B1088 - 1337

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