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- PDB-6f9i: Crystal structure of KLC2 bound to the second tryptophan-acidic m... -

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Basic information

Entry
Database: PDB / ID: 6f9i
TitleCrystal structure of KLC2 bound to the second tryptophan-acidic motif peptide from calsyntenin-1
Components
  • Calsyntenin-1
  • Kinesin light chain 2
KeywordsMOTOR PROTEIN / kinesin / cargo / activation / transport
Function / homology
Function and homology information


X11-like protein binding / : / postsynaptic endosome / : / neurotransmitter receptor transport to postsynaptic membrane / vesicle-mediated transport in synapse / regulation of synapse maturation / lysosome localization / positive regulation of synapse assembly / kinesin complex ...X11-like protein binding / : / postsynaptic endosome / : / neurotransmitter receptor transport to postsynaptic membrane / vesicle-mediated transport in synapse / regulation of synapse maturation / lysosome localization / positive regulation of synapse assembly / kinesin complex / microtubule-based movement / homophilic cell adhesion via plasma membrane adhesion molecules / kinesin binding / GABA-ergic synapse / positive regulation of synaptic transmission / regulation of cell growth / intracellular calcium ion homeostasis / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / microtubule / membrane => GO:0016020 / postsynaptic density / Golgi membrane / glutamatergic synapse / calcium ion binding / endoplasmic reticulum membrane / cell surface / mitochondrion / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Calsyntenin / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Calsyntenin / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Kinesin light chain / Calsyntenin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.993 Å
AuthorsCockburn, J.J.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRG150205 United Kingdom
CitationJournal: Structure / Year: 2018
Title: Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3.
Authors: Cockburn, J.J.B. / Hesketh, S.J. / Mulhair, P. / Thomsen, M. / O'Connell, M.J. / Way, M.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin light chain 2
X: Calsyntenin-1
B: Kinesin light chain 2
C: Calsyntenin-1


Theoretical massNumber of molelcules
Total (without water)70,2764
Polymers70,2764
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-18 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.442, 75.442, 303.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Kinesin light chain 2 / Klc2 protein


Mass: 33337.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klc2, mCG_8395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YS4
#2: Protein/peptide Calsyntenin-1 / Alcadein-alpha / Alc-alpha


Mass: 1799.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9EPL2

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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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.893 M sodium potassium tartrate, 0.2 M NaCl, 0.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.99→44.46 Å / Num. obs: 8641 / % possible obs: 94.9 % / Redundancy: 2.8 % / Net I/σ(I): 6.28
Reflection shellResolution: 3.99→4.21 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zfw

3zfw


Resolution: 3.993→44.458 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.33
RfactorNum. reflection% reflection
Rfree0.2734 410 4.75 %
Rwork0.2531 --
obs0.254 8630 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.993→44.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 0 0 4328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054399
X-RAY DIFFRACTIONf_angle_d0.9765937
X-RAY DIFFRACTIONf_dihedral_angle_d17.7881678
X-RAY DIFFRACTIONf_chiral_restr0.039659
X-RAY DIFFRACTIONf_plane_restr0.004772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9931-4.57040.36621370.33732713X-RAY DIFFRACTION97
4.5704-5.75630.29771380.31512750X-RAY DIFFRACTION96
5.7563-44.46110.23521350.20782757X-RAY DIFFRACTION91
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)
10.77070.50350.73250.3111-0.74582.6656-0.21450.26470.01210.0079-0.1641-0.12150.2591-0.0129-0.191.94170.4585-0.07821.873-0.08521.870951.703-32.184247.8914
20.8676-0.47170.3043-0.44420.91176.6440.1756-0.08120.08070.2558-0.1939-0.22860.3352-0.57390.18061.9199-0.1806-0.0441.69250.13631.815226.1327-37.9533-8.1001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain C
2X-RAY DIFFRACTION2Chain B or chain X

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