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- PDB-4rcw: Crystal structure of human Slitrk1 -

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Basic information

Entry
Database: PDB / ID: 4rcw
TitleCrystal structure of human Slitrk1
ComponentsSLIT and NTRK-like protein 1
KeywordsSIGNALING PROTEIN / Leucine rich-repeat / synaptic adhesion
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / vocalization behavior / norepinephrine metabolic process / positive regulation of axonogenesis / positive regulation of synapse assembly / neuron projection extension / homeostatic process / adult behavior / regulation of presynapse assembly ...Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / vocalization behavior / norepinephrine metabolic process / positive regulation of axonogenesis / positive regulation of synapse assembly / neuron projection extension / homeostatic process / adult behavior / regulation of presynapse assembly / synapse assembly / axonogenesis / postsynaptic density membrane / GABA-ergic synapse / multicellular organism growth / endocytosis / gene expression / synapse / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
SLIT and NTRK-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1925 Å
AuthorsKim, H.M. / Park, B.S. / Kim, D. / Lee, S.G.
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion.
Authors: Um, J.W. / Kim, K.H. / Park, B.S. / Choi, Y. / Kim, D. / Kim, C.Y. / Kim, S.J. / Kim, M. / Ko, J.S. / Lee, S.G. / Choii, G. / Nam, J. / Heo, W.D. / Kim, E. / Lee, J.O. / Ko, J. / Kim, H.M.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SLIT and NTRK-like protein 1
B: SLIT and NTRK-like protein 1


Theoretical massNumber of molelcules
Total (without water)54,6532
Polymers54,6532
Non-polymers00
Water543
1
A: SLIT and NTRK-like protein 1


Theoretical massNumber of molelcules
Total (without water)27,3271
Polymers27,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SLIT and NTRK-like protein 1


Theoretical massNumber of molelcules
Total (without water)27,3271
Polymers27,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.607, 69.607, 409.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein SLIT and NTRK-like protein 1 / Leucine-rich repeat-containing protein 12


Mass: 27326.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLITRK1, KIAA1910, LRRC12, UNQ233/PRO266 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PX8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na-citrate, pH 5.5, 16% isopropanol, and 12% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99362 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99362 Å / Relative weight: 1
ReflectionResolution: 3.1925→50 Å / Num. all: 10729 / Num. obs: 10569 / % possible obs: 99 % / Observed criterion σ(I): 3.4 / Redundancy: 12.6 % / Biso Wilson estimate: 107 Å2 / Net I/σ(I): 35
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.1925-3.261100
3.26-3.31198.5
3.31-3.38198.4
3.38-3.45198.8
3.45-3.52198.1
3.52-3.6199
3.6-3.69199.2
3.69-3.79199.4
3.79-3.91198.1
3.91-4.03199.6
4.03-4.18199
4.18-4.34198.7
4.34-4.54199.8
4.54-4.78198.9
4.78-5.08199.6
5.08-5.47199.4
5.47-6.02199.1
6.02-6.89199.5
6.89-8.67199.3
8.67-50198.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M18

3m18


Resolution: 3.1925→48.567 Å / SU ML: 0.42 / σ(F): 1.45 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 509 4.82 %
Rwork0.2586 --
obs0.2605 10568 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1925→48.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 0 3 3725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023797
X-RAY DIFFRACTIONf_angle_d0.65136
X-RAY DIFFRACTIONf_dihedral_angle_d11.0771403
X-RAY DIFFRACTIONf_chiral_restr0.023587
X-RAY DIFFRACTIONf_plane_restr0.003660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1925-3.51370.34121210.30932326X-RAY DIFFRACTION95
3.5137-4.02190.30491280.26512458X-RAY DIFFRACTION99
4.0219-5.06640.31021280.22912526X-RAY DIFFRACTION100
5.0664-48.57270.27511320.26312749X-RAY DIFFRACTION100
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)
1-0.00210.00630.0066-0.0006-0.004-0.0050.0515-0.0675-0.12020.08710.05250.12260.0328-0.093901.11410.2848-0.14270.7441-0.09780.569.878619.2537-4.3838
2-0.00090.0160.01480.00570.01330.01260.01660.02210.1165-0.04190.0156-0.052-0.002-0.0449-01.13090.3463-0.27590.4949-1.0824-0.12489.30949.4072.895
30.0078-0.027-0.01910.01230.00670.0219-0.0290.0815-0.3555-0.13860.29650.2426-0.02390.010701.19050.2868-0.20070.394-0.49470.464616.435312.71065.2547
4-0.00140.002-0.01490.01540.00780.0079-0.20620.1457-0.1557-0.1824-0.15240.21090.10030.068900.94950.0718-0.15420.1276-0.30960.650819.930212.289511.0117
50.0515-0.0735-0.02470.065-0.02360.01490.3978-0.8842-0.5647-0.3947-0.3792-0.1785-0.01550.095400.58690.17-0.00040.0544-0.260.502824.244222.453921.4059
6-0.0025-0.0110.00360.00530.01320.0018-0.0895-0.064-0.12730.0189-0.0692-0.0678-0.0031-0.012600.71060.2219-0.02790.3503-0.56420.167720.728227.511939.885
70.01960.02480.01730.02690.00670.0151-0.3143-0.11850.19560.05340.10510.0419-0.3362-0.056200.84820.0281-0.02660.4014-0.19730.665420.932734.866240.5136
80.00010.002-0.0091-0.00110.0056-0.00450.10150.01050.0539-0.03920.041-0.02960.05060.0225-01.28440.03010.32460.8845-0.32120.923824.186436.5703-0.7266
90.00450.0070.00430.0031-0.02330.0089-0.1451-0.04960.0181-0.1107-0.1779-0.0446-0.03540.0344-01.3666-0.01460.10860.39880.05880.866320.471545.07876.0076
10-0.00610.0093-0.03590.0079-0.04360.0117-0.31750.17880.0143-0.0429-0.1792-0.2877-0.05090.192402.03680.17150.1601-0.02130.46940.399811.29843.69227.3625
11-0.0134-0.01840.01260.0016-0.02670.0260.0406-0.16150.0440.1482-0.0929-0.0547-0.06340.000601.68390.6759-0.020.54380.2740.25356.555838.218811.9542
12-0.0079-0.00230.00390.00870.00170.01340.04590.09360.01320.01420.0993-0.08380.0373-0.090501.20610.4926-0.11580.7504-0.00520.44262.507235.57727.2988
13-0.0013-0.06680.01530.0427-0.03270.03120.13350.09080.01590.0087-0.19130.1377-0.01660.0723-00.95280.4539-0.21940.3044-0.05980.497-0.493433.261818.3729
14-0.0069-0.01220.0080.01150.0107-0.00430.0630.08330.09760.05760.18060.0656-0.0678-0.0675-00.47060.9324-0.3604-0.3592-0.23120.9333-6.299425.671921.9673
150.00180.00140.0031-0.0139-0.00630.0020.00940.1028-0.03970.0220.00650.0237-0.02020.0939-00.71650.107-0.04080.6262-0.06690.5008-4.432727.069434.0965
16-0.0139-0.02650.00440.0363-0.00720.0074-0.15820.05430.056-0.02890.16520.16850.09250.0649-00.64560.2374-0.06720.51620.01230.8705-4.922319.729334.4104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 342 through 358 )
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 376 )
3X-RAY DIFFRACTION3chain 'A' and (resid 377 through 402 )
4X-RAY DIFFRACTION4chain 'A' and (resid 403 through 422 )
5X-RAY DIFFRACTION5chain 'A' and (resid 423 through 525 )
6X-RAY DIFFRACTION6chain 'A' and (resid 526 through 537 )
7X-RAY DIFFRACTION7chain 'A' and (resid 538 through 579 )
8X-RAY DIFFRACTION8chain 'B' and (resid 343 through 358 )
9X-RAY DIFFRACTION9chain 'B' and (resid 359 through 378 )
10X-RAY DIFFRACTION10chain 'B' and (resid 379 through 422 )
11X-RAY DIFFRACTION11chain 'B' and (resid 423 through 440 )
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 453 )
13X-RAY DIFFRACTION13chain 'B' and (resid 454 through 505 )
14X-RAY DIFFRACTION14chain 'B' and (resid 506 through 525 )
15X-RAY DIFFRACTION15chain 'B' and (resid 526 through 537 )
16X-RAY DIFFRACTION16chain 'B' and (resid 538 through 579 )

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