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- PDB-3r05: Structure of neurexin 1 alpha (domains LNS1-LNS6), with splice in... -

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Basic information

Entry
Database: PDB / ID: 3r05
TitleStructure of neurexin 1 alpha (domains LNS1-LNS6), with splice insert SS3
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-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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsVenugopal, V. / Rudenko, G.
CitationJournal: Structure / Year: 2011
Title: The structure of neurexin 1α reveals features promoting a role as synaptic organizer
Authors: Chen, F. / Venugopal, V. / Murray, B. / Rudenko, G.
History
DepositionMar 7, 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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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: Neurexin-1-alpha
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,8704
Polymers277,0222
Non-polymers8492
Water00
1
A: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9352
Polymers138,5111
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)138,9352
Polymers138,5111
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.030, 114.574, 160.129
Angle α, β, γ (deg.)89.600, 89.980, 87.960
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 - 325
2111B281 - 325
1211A327 - 368
2211B327 - 368
1311A370 - 456
2311B370 - 456
1416A457 - 459
2416B457 - 459
1511A460 - 464
2511B460 - 464
1611A466 - 468
2611B466 - 468
1716A469 - 470
2716B469 - 470
1811A471 - 475
2811B471 - 475
1911A477 - 478
2911B477 - 478
11011A480 - 482
21011B480 - 482
11116A483 - 485
21116B483 - 485
1121A486 - 534
2121B486 - 534
1221A536 - 537
2221B536 - 537
1321A539 - 547
2321B539 - 547
1421A549 - 552
2421B549 - 552
1521A554 - 586
2521B554 - 586
1621A588 - 628
2621B588 - 628
1721A630 - 658
2721B630 - 658
1826A659 - 665
2826B659 - 665
1921A666 - 677
2921B666 - 677
11026A678 - 680
21026B678 - 680
1131A681 - 716
2131B681 - 716
1231A718 - 722
2231B718 - 722
1141A723 - 725
2141B723 - 725
1241A727 - 790
2241B727 - 790
1341A801 - 823
2341B801 - 823
1441A825 - 909
2441B825 - 909
1151A910 - 1024
2151B910 - 1024
1251A1026 - 1050
2251B1026 - 1050
1351A1052 - 1087
2351B1052 - 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: 138510.750 Da / Num. of mol.: 2 / Fragment: UNP residues 31-1355 / Mutation: 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)], AND SS4 [DEL(1248-1278)]. THE SPLICE INSERT SS3 IS PRESENT [CONTAINING RESIDUES(790-799) WITH D790G]

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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: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 14.13 / Number: 306149 / Rmerge(I) obs: 0.09 / Χ2: 1.24 / D res high: 2.95 Å / D res low: 50 Å / Num. obs: 89668 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
85096.110.0451.2033.4
6.35898.910.0461.1683.4
5.556.3599.310.0551.3573.5
5.045.5599.310.0551.2973.5
4.685.0499.210.0541.2413.5
4.414.689910.0571.3853.5
4.194.419910.0681.4073.5
44.1998.910.0861.1743.5
3.85498.810.0971.2463.5
3.723.8598.810.121.2953.5
3.63.7298.510.1541.4383.4
3.53.698.810.1581.3043.4
3.413.598.410.2061.2713.5
3.323.4198.510.2391.1783.5
3.253.3298.510.2911.1693.5
3.183.2598.310.3541.1023.4
3.113.1898.110.3911.13.4
3.063.1197.910.5071.1273.3
33.0697.310.4951.1223.2
2.95395.610.5321.0523.1
ReflectionResolution: 2.95→50 Å / Num. obs: 89668 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.235 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-33.10.53243561.052195.6
3-3.063.20.49544951.122197.3
3.06-3.113.30.50743621.127197.9
3.11-3.183.40.39145231.1198.1
3.18-3.253.40.35444691.102198.3
3.25-3.323.50.29144661.169198.5
3.32-3.413.50.23945361.178198.5
3.41-3.53.50.20644161.271198.4
3.5-3.63.40.15845611.304198.8
3.6-3.723.40.15444661.438198.5
3.72-3.853.50.1245181.295198.8
3.85-43.50.09745121.246198.8
4-4.193.50.08644931.174198.9
4.19-4.413.50.06845341.407199
4.41-4.683.50.05745321.385199
4.68-5.043.50.05444891.241199.2
5.04-5.553.50.05545511.297199.3
5.55-6.353.50.05544981.357199.3
6.35-83.40.04645031.168198.9
8-503.40.04543881.203196.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QCW

3qcw


Resolution: 2.95→44.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2446 / WRfactor Rwork: 0.2403 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8169 / SU B: 31.451 / SU ML: 0.253 / SU R Cruickshank DPI: 0.6154 / SU Rfree: 0.3254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 4654 5.2 %RANDOM
Rwork0.2083 ---
obs0.2097 89495 98.15 %-
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: 210.55 Å2 / Biso mean: 92.1204 Å2 / Biso min: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--7.06 Å20.84 Å2-1.09 Å2
2---2.87 Å2-0.42 Å2
3---9.88 Å2
Refinement stepCycle: LAST / Resolution: 2.95→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15466 0 56 0 15522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02215852
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.95521508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.09652012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8324.525716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69152600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3171586
X-RAY DIFFRACTIONr_chiral_restr0.1390.22412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212044
X-RAY DIFFRACTIONr_nbd_refined0.260.26623
X-RAY DIFFRACTIONr_nbtor_refined0.3360.210706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2508
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.29
X-RAY DIFFRACTIONr_mcbond_it0.7171.510184
X-RAY DIFFRACTIONr_mcangle_it1.187215996
X-RAY DIFFRACTIONr_scbond_it1.90236370
X-RAY DIFFRACTIONr_scangle_it2.7874.55512
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
11316TIGHT POSITIONAL0.040.05
155LOOSE POSITIONAL0.25
11316TIGHT THERMAL0.080.5
155LOOSE THERMAL0.1810
21390TIGHT POSITIONAL0.040.05
272LOOSE POSITIONAL0.265
21390TIGHT THERMAL0.090.5
272LOOSE THERMAL1.3810
3313TIGHT POSITIONAL0.040.05
3313TIGHT THERMAL0.080.5
41384TIGHT POSITIONAL0.050.05
41384TIGHT THERMAL0.150.5
51353TIGHT POSITIONAL0.050.05
51353TIGHT THERMAL0.150.5
6305TIGHT POSITIONAL0.050.05
6305TIGHT THERMAL0.110.5
71384TIGHT POSITIONAL0.040.05
71384TIGHT THERMAL0.10.5
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 338 -
Rwork0.315 5890 -
all-6228 -
obs--93.35 %
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)
18.6427-4.11242.14067.4248-3.24433.0815-0.03160.12120.56560.2757-0.3952-0.0693-0.7765-0.07610.42680.9113-0.0337-0.03451.0177-0.2198-0.3595-7.427112.9297-18.1365
27.3844-1.1469-1.47273.63750.76124.2335-0.0644-0.51530.55040.513-0.0551-0.3864-0.55070.3920.11950.42720.0257-0.11460.65030.0165-0.4864-9.22989.0965-50.2641
33.6955-0.8196-2.64490.66853.926524.8087-0.2073-1.0817-0.05530.9439-0.0130.0668-0.1661-1.52150.2203-0.0370.17610.10490.5512-0.0789-0.1152-31.71869.7343-66.1543
45.18290.55340.27822.8303-0.18424.5203-0.005-0.8937-0.0760.52460.00660.0130.14040.0666-0.0016-0.40670.06490.0198-0.4090.0473-0.5177-11.45370.1541-80.3642
54.80130.4666-0.49383.77570.59161.9454-0.0186-0.0024-0.47630.0305-0.035-0.34460.20080.19810.0536-0.601-0.02760.0164-0.6803-0.0219-0.2969-16.9873-13.8322-107.3818
62.08880.83750.581113.7528-3.66211.2924-0.32870.39180.8668-1.27710.58320.8718-0.1787-0.5906-0.2545-0.19280.0693-0.0103-0.41880.16180.0079-7.325524.787-115.1462
76.565-1.39661.69586.1028-0.13934.4094-0.04940.12850.8406-0.11660.01-0.2538-0.93320.04280.0394-0.0013-0.06370.0956-0.65290.08870.2555.996644.6514-108.6841
89.52555.3283-2.02357.9814-3.01743.00180-0.1098-0.634-0.2949-0.310.05880.75840.00730.310.9238-0.00080.00451.0431-0.2416-0.485-37.9787-15.4192-190.087
97.47710.98841.06394.09250.98494.5352-0.07130.6684-0.5255-0.6198-0.0239-0.42710.56770.35820.09520.4014-0.08990.11280.5980.0348-0.4791-39.7965-11.6233-157.9843
102.62720.82213.00040.93224.787525.371-0.13130.95130.1997-0.9139-0.1131-0.05640.1726-1.56960.2443-0.0564-0.1802-0.09640.4866-0.0763-0.1362-62.2348-12.226-142.0562
114.3485-0.63870.0352.29870.04074.5685-0.04560.83140.0773-0.4277-0.0037-0.0558-0.12980.10410.0493-0.4215-0.0716-0.0162-0.47230.0412-0.4354-41.9666-2.7439-127.8597
125.2144-0.53260.26653.91840.68771.91640.0051-0.05830.51110.02760.0379-0.3668-0.20460.2013-0.0431-0.60320.0284-0.0118-0.6616-0.0381-0.3289-47.512611.2337-100.8102
133.1374-3.05790.813813.1055-3.75741.7973-0.5547-0.5524-1.13681.27990.69441.17960.2832-0.6716-0.1397-0.2228-0.07320.0873-0.31460.18270.0391-37.7376-27.5451-93.1555
148.86911.2524-2.32216.2535-0.43584.6718-0.1645-0.1718-1.03610.19940.01050.24921.016-0.13590.154-0.00570.01090.0158-0.64080.10380.3494-24.0746-47.3412-99.3662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A281 - 485
2X-RAY DIFFRACTION2A486 - 679
3X-RAY DIFFRACTION3A680 - 722
4X-RAY DIFFRACTION4A723 - 909
5X-RAY DIFFRACTION5A910 - 1087
6X-RAY DIFFRACTION6A1088 - 1130
7X-RAY DIFFRACTION7A1131 - 1337
8X-RAY DIFFRACTION8B281 - 485
9X-RAY DIFFRACTION9B486 - 679
10X-RAY DIFFRACTION10B680 - 722
11X-RAY DIFFRACTION11B723 - 909
12X-RAY DIFFRACTION12B910 - 1087
13X-RAY DIFFRACTION13B1088 - 1130
14X-RAY DIFFRACTION14B1131 - 1337

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