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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 / Cell Adhesion / Synapse
Function / homologyConcanavalin A-like lectin/glucanase domain superfamily / Aspartic acid and asparagine hydroxylation site. / EGF-like domain profile. / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Laminin G domain / Neurexin/syndecan/glycophorin C / Laminin G domain profile. / Syndecan/Neurexin domain / Neurexin ...Concanavalin A-like lectin/glucanase domain superfamily / Aspartic acid and asparagine hydroxylation site. / EGF-like domain profile. / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Laminin G domain / Neurexin/syndecan/glycophorin C / Laminin G domain profile. / Syndecan/Neurexin domain / Neurexin / EGF-like domain / Syndecan domain / Laminin G domain / neuroligin family protein binding / presynaptic membrane / cell junction / cell adhesion / integral component of membrane / metal ion binding / Neurexin-1
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.84 Å resolution
AuthorsMisra, A. / Rudenko, G.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2018 / Release: Sep 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 19, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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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
Polyers89,0342
Non-polymers00
Water21612
1
A: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polyers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polyers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 1 21 1

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Components

#1: Protein/peptide 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: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid name: pGEX-KG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q28146
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Formula: H2O / Water

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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 / Density percent sol: 64.39 % / Mosaicity: 1.742 deg.
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 21-ID-D / Synchrotron site: APS / Beamline: 21-ID-D / Wavelength: 1.10208
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Mar 21, 2008
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10208 Å / Relative weight: 1
ReflectionD resolution high: 2.84 Å / D resolution low: 50.01 Å / Number obs: 28540 / Rmerge I obs: 0.091 / Rpim I all: 0.058 / Rrim I all: 0.108 / Chi squared: 1.469 / NetI over sigmaI: 15.2 / Redundancy: 3.4 % / Percent possible obs: 98.4
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRpim I allRrim I allChi squaredRedundancyPercent possible all
0.5202.8402.9502.225550.7150.3910.6541.1782.40089.100
0.3912.9503.07027740.7960.2930.4921.3922.70096.400
0.2753.0703.21028220.9020.1930.3381.3252.90098.800
0.1743.2103.38028960.9660.1130.2081.4183.30099.900
0.1303.3803.59028790.9840.0790.1531.4913.70099.900
0.1053.5903.87028760.9890.0640.1231.6613.70099.900
0.0823.8704.26028930.9910.0500.0961.5023.800100.000
0.0674.2604.87029200.9910.0410.0791.4553.700100.000
0.0634.8706.14029290.9920.0380.0741.5193.700100.000
0.0626.14050.01029960.9940.0370.0731.5073.60099.500

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
HKL-2000data reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/program
PHASERphasingRandy J. Readcimr-phaser[at]lists.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk/phaser/program
REFMAC5.8.0158refinementGarib N. Murshudovgarib[at]ysbl.york.ac.ukhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramFortran_77
PDB_EXTRACT3.24data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++Sep. 1, 2017
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QCW
Correlation coeff Fo to Fc: 0.923 / Correlation coeff Fo to Fc free: 0.889
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Overall SU B: 35.561 / Overall SU ML: 0.307 / Overall SU R Cruickshank DPI: 0.7583 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.758 / Overall ESU R Free: 0.341
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 138.21 Å2 / B iso mean: 52.259 Å2 / B iso min: 24.48 Å2 / Aniso B11: -1.71 Å2 / Aniso B12: 0 Å2 / Aniso B13: -0.39 Å2 / Aniso B22: -0.57 Å2 / Aniso B23: - Å2 / Aniso B33: 2.3 Å2
Least-squares processR factor R free: 0.2548 / R factor R work: 0.2216 / R factor obs: 0.2233 / Highest resolution: 2.84 Å / Lowest resolution: 50.01 Å / Number reflection R free: 1418 / Number reflection obs: 27112 / Percent reflection R free: 5 / Percent reflection obs: 97.88
Refine hist #finalHighest resolution: 2.84 Å / Lowest resolution: 50.01 Å / B iso mean solvent: 42.12 / Number residues total: 762
Number of atoms included #finalProtein: 5730 / Nucleic acid: 0 / Ligand: 0 / Solvent: 12 / Total: 5742
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195857
X-RAY DIFFRACTIONr_bond_other_d0.0010.0205216
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9567970
X-RAY DIFFRACTIONr_angle_other_deg0.8093.00012073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3005.000758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36224.733243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42615.000900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.05415.00019
X-RAY DIFFRACTIONr_chiral_restr0.0900.200910
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0201180
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
Refine LS shellHighest resolution: 2.837 Å / R factor R free: 0.339 / R factor R free error: 0 / R factor R work: 0.312 / Lowest resolution: 2.911 Å / Number reflection R free: 75 / Number reflection R work: 1668 / Number reflection all: 1743 / Total number of bins used: 20 / Percent reflection obs: 82.1
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
15.2153-1.07643.52333.3341-1.38294.9136-0.1320-0.2250-0.2281-0.3245-0.0278-0.13780.1433-0.08500.15970.19700.0528-0.07470.0370-0.01320.153160.9817-2.572731.2217
20.7574-0.88711.18463.8350-2.53205.4667-0.16140.09610.09480.0734-0.1277-0.2364-0.27780.39690.28910.4021-0.0009-0.22380.12250.03930.218948.022020.03671.9804
36.6581-0.91142.62952.5006-0.77622.4597-0.1664-0.33120.5166-0.11630.0072-0.2090-0.4035-0.32150.15920.15540.0462-0.09090.0945-0.00550.314588.62050.216050.6240
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
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A279A4851
2A486A6732
3B278B4853
4B486B6744

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