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- PDB-5fjy: Crystal structure of mouse kinesin light chain 2 (residues 161-480) -

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Basic information

Entry
Database: PDB / ID: 5fjy
TitleCrystal structure of mouse kinesin light chain 2 (residues 161-480)
Components
  • KINESIN LIGHT CHAIN 2
  • UNKNOWN PEPTIDE
KeywordsPROTEIN TRANSPORT / MOLECULAR TRANSPORT / TPR DOMAINS / AUTOINHIBITION
Function / homology
Function and homology information


RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / lysosome localization / MHC class II antigen presentation / axo-dendritic transport / kinesin complex / microtubule-based movement / kinesin binding ...RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / lysosome localization / MHC class II antigen presentation / axo-dendritic transport / kinesin complex / microtubule-based movement / kinesin binding / microtubule / neuron projection / lysosomal membrane / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Kinesin light chain 2 / Kinesin light chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsPernigo, S. / Yip, Y.Y. / Sanger, A. / Xu, M. / Dodding, M.P. / Steiner, R.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: The Light Chains of Kinesin-1 are Autoinhibited.
Authors: Yip, Y.Y. / Pernigo, S. / Sanger, A. / Xu, M. / Parsons, M. / Steiner, R.A. / Dodding, M.P.
#1: Journal: Science / Year: 2013
Title: Structural Basis for Kinesin-1:Cargo Recognition
Authors: Pernigo, S. / Lamprecht, A. / Steiner, R.A. / Dodding, M.P.
History
DepositionOct 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 16, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN LIGHT CHAIN 2
B: KINESIN LIGHT CHAIN 2
C: KINESIN LIGHT CHAIN 2
D: UNKNOWN PEPTIDE
E: UNKNOWN PEPTIDE
F: UNKNOWN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)110,4446
Polymers110,4446
Non-polymers00
Water00
1
A: KINESIN LIGHT CHAIN 2
B: KINESIN LIGHT CHAIN 2
D: UNKNOWN PEPTIDE
E: UNKNOWN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)73,6294
Polymers73,6294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint1.3 kcal/mol
Surface area33070 Å2
MethodPQS
2
C: KINESIN LIGHT CHAIN 2
F: UNKNOWN PEPTIDE

C: KINESIN LIGHT CHAIN 2
F: UNKNOWN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)73,6294
Polymers73,6294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area3590 Å2
ΔGint-8.8 kcal/mol
Surface area32870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)148.700, 86.280, 111.740
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KINESIN LIGHT CHAIN 2 / KLC2


Mass: 36370.984 Da / Num. of mol.: 3 / Fragment: TPR DOMAIN WITH N-TERMINAL EXTENSION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91YS4, UniProt: O88448*PLUS
#2: Protein/peptide UNKNOWN PEPTIDE


Mass: 443.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: PEPTIDE MAY BE PART OF TPR N-TERMINAL EXTENSION / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
Has protein modificationY
Nonpolymer detailsUNKNOWN AMINO ACID (UNK): RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL ...UNKNOWN AMINO ACID (UNK): RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION OF THE DATA WE ARE UNABLE TO DEFINE THEIR CORRECT IDENTITY.
Sequence detailsTHE FIRST FOUR AMINO ACIDS DERIVE FROM THE CLONING STRATEGY

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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: 3.25 Å3/Da / Density % sol: 62.15 % / Description: NONE
Crystal growpH: 6.5
Details: 8% (W/V) PGA-LM 0.3 M NA-MALONATE 0.1 M NA-CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 4→42.88 Å / Num. obs: 11813 / % possible obs: 98.4 % / Observed criterion σ(I): -1 / Redundancy: 3 % / Biso Wilson estimate: 163 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.9
Reflection shellResolution: 4→4.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 0.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CEQ AND 3ZFW

3ceq

3zfw


Resolution: 4→42.88 Å / Cor.coef. Fo:Fc: 0.9119 / Cor.coef. Fo:Fc free: 0.9143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.745
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES LABELLED AS UNK ARE BELIEVED TO BE PART OF THE TPR N-TERMINAL EXTENSION. DUE TO THE LOW RESOLUTION OF THE DATA WE ARE UNABLE TO DEFINE THEIR CORRECT IDENTITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 544 4.61 %RANDOM
Rwork0.2328 ---
obs0.2343 11801 98.28 %-
Displacement parametersBiso mean: 266.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.5491 Å20 Å2-95.4686 Å2
2--0.8546 Å20 Å2
3----7.4037 Å2
Refine analyzeLuzzati coordinate error obs: 0.799 Å
Refinement stepCycle: LAST / Resolution: 4→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 0 0 6405
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016510HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2349SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes933HARMONIC5
X-RAY DIFFRACTIONt_it6510HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion23.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion831SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7573SEMIHARMONIC4
LS refinement shellResolution: 4→4.38 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2777 160 5.68 %
Rwork0.2505 2657 -
all0.2521 2817 -
obs--98.53 %
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)
18.7631-3.1695-2.04472.53121.15761.20010.1129-0.5622-0.42440.1045-0.5443-0.5349-0.40220.08730.4314-0.17260.1286-0.1177-0.30410.17360.2796-33.964811.634.8941
27.5691-0.07392.98640.3610.00019.32070.0885-0.4596-0.46790.1470.3449-0.12090.6237-0.6191-0.4334-0.2753-0.128-0.09360.3046-0.1732-0.3324-75.47749.180217.198
37.50892.70982.788301.82659.43320.0744-0.1180.3027-0.4373-0.5059-0.2628-0.60390.53360.43160.2987-0.17370.06280.30590.1285-0.3001-62.592241.243547.0521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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