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- PDB-6cw1: Crystal structure of Neurexin-1 alpha ectodomain fragment, L2-L3 -

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Basic information

Entry
Database: PDB / ID: 6cw1
TitleCrystal structure of Neurexin-1 alpha ectodomain fragment, L2-L3
ComponentsNeurexin-1
KeywordsCELL ADHESION / LNS domain / Beta-Sandwich / Synapse
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 / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-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 / 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 / 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: 2.84 Å
AuthorsMisra, A. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
CitationJournal: J Mol Biol / Year: 2018
Title: Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer.
Authors: Jianfang Liu / Anurag Misra / M V V V Sekhar Reddy / Mark Andrew White / Gang Ren / Gabby Rudenko /
Abstract: α-Neurexins are synaptic organizing molecules implicated in neuropsychiatric disorders. They bind and arrange an array of different partners in the synaptic cleft. The extracellular region of ...α-Neurexins are synaptic organizing molecules implicated in neuropsychiatric disorders. They bind and arrange an array of different partners in the synaptic cleft. The extracellular region of neurexin 1α (n1α) contains six LNS domains (L1-L6) interspersed by three Egf-like repeats. N1α must encode highly evolved structure-function relationships in order to fit into the narrow confines of the synaptic cleft, and also recruit its large, membrane-bound partners. Internal molecular flexibility could provide a solution; however, it is challenging to delineate because currently no structural methods permit high-resolution structure determination of large, flexible, multi-domain protein molecules. To investigate the structural plasticity of n1α, in particular the conformation of domains that carry validated binding sites for different protein partners, we used a panel of structural techniques. Individual particle electron tomography revealed that the N-terminally and C-terminally tethered domains, L1 and L6, have a surprisingly limited range of conformational freedom with respect to the linear central core containing L2 through L5. A 2.8-Å crystal structure revealed an unexpected arrangement of the L2 and L3 domains. Small-angle X-ray scattering and electron tomography indicated that incorporation of the alternative splice insert SS6 relieves the restricted conformational freedom between L5 and L6, suggesting that SS6 may work as a molecular toggle. The architecture of n1α thus encodes a combination of rigid and flexibly tethered domains that are uniquely poised to work together to promote its organizing function in the synaptic cleft, and may permit allosterically regulated and/or concerted protein partner binding.
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurexin-1
B: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)89,0342
Polymers89,0342
Non-polymers00
Water21612
1
A: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polymers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polymers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.144, 62.901, 113.061
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 279 - 672 / Label seq-ID: 22 - 400

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Neurexin-1 / / Neurexin I-alpha / Neurexin-1-alpha


Mass: 44517.121 Da / Num. of mol.: 2 / Fragment: Alpha fragment L2-L3, residues 258-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid: pGEX-KG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q28146
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.45 Å3/Da / Density % sol: 64.39 % / Mosaicity: 1.742 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.9 M NaCITRATE, 0.1 M TRIS PH 8.0, 5 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.10208 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10208 Å / Relative weight: 1
ReflectionResolution: 2.84→50.01 Å / Num. obs: 28540 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Χ2: 1.469 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.84-2.952.40.522.225550.7150.3910.6541.17889.1
2.95-3.072.70.39127740.7960.2930.4921.39296.4
3.07-3.212.90.27528220.9020.1930.3381.32598.8
3.21-3.383.30.17428960.9660.1130.2081.41899.9
3.38-3.593.70.1328790.9840.0790.1531.49199.9
3.59-3.873.70.10528760.9890.0640.1231.66199.9
3.87-4.263.80.08228930.9910.050.0961.502100
4.26-4.873.70.06729200.9910.0410.0791.455100
4.87-6.143.70.06329290.9920.0380.0741.519100
6.14-50.013.60.06229960.9940.0370.0731.50799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QCW

3qcw


Resolution: 2.84→50.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 35.561 / SU ML: 0.307 / SU R Cruickshank DPI: 0.7583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.758 / ESU R Free: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1418 5 %RANDOM
Rwork0.2216 ---
obs0.2233 27112 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.21 Å2 / Biso mean: 52.259 Å2 / Biso min: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.39 Å2
2---0.57 Å2-0 Å2
3---2.3 Å2
Refinement stepCycle: final / Resolution: 2.84→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 0 12 5742
Biso mean---42.12 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195857
X-RAY DIFFRACTIONr_bond_other_d0.0010.025216
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9567970
X-RAY DIFFRACTIONr_angle_other_deg0.809312073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36224.733243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42615900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0541519
X-RAY DIFFRACTIONr_chiral_restr0.090.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
Refine LS restraints NCS

Ens-ID: 1 / Number: 22294 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.837→2.911 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 75 -
Rwork0.312 1668 -
all-1743 -
obs--82.1 %
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)
15.2153-1.07643.52333.3341-1.38294.9136-0.132-0.225-0.2281-0.3245-0.0278-0.13780.1433-0.0850.15970.1970.0528-0.07470.037-0.01320.153160.9817-2.572731.2217
20.7574-0.88711.18463.835-2.5325.4667-0.16140.09610.09480.0734-0.1277-0.2364-0.27780.39690.28910.4021-0.0009-0.22380.12250.03930.218948.02220.03671.9804
36.6581-0.91142.62952.5006-0.77622.4597-0.1664-0.33120.5166-0.11630.0072-0.209-0.4035-0.32150.15920.15540.0462-0.09090.0945-0.00550.314588.62050.21650.624
46.4086-2.0189-0.97773.8886-0.04340.72650.08620.4989-0.3071-0.1683-0.08240.25230.0915-0.0866-0.00390.08770.0043-0.09080.0421-0.00680.2485120.6521-22.476852.1975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 485
2X-RAY DIFFRACTION2A486 - 673
3X-RAY DIFFRACTION3B278 - 485
4X-RAY DIFFRACTION4B486 - 674

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