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- PDB-7aie: Crystal structure of a truncated form of the KLC1-TPR domain ([A1... -

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Basic information

Entry
Database: PDB / ID: 7aie
TitleCrystal structure of a truncated form of the KLC1-TPR domain ([A1-B5] fragment) - Monoclinic crystal form
ComponentsKinesin light chain 1
KeywordsMOTOR PROTEIN / Kinesin Light Chain / kinesin1 / TPR domain / Kif5 / accesosry protein
Function / homology
Function and homology information


Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / MHC class II antigen presentation / Signaling by ALK fusions and activated point mutants ...Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / MHC class II antigen presentation / Signaling by ALK fusions and activated point mutants / growth cone / cytoplasmic vesicle / microtubule / cell adhesion / membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Kinesin light chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.287 Å
AuthorsMenetrey, J. / Llinas, P.
CitationJournal: To Be Published
Title: Structural investigations of the dynamics of the TPR domain of kinesin light chain
Authors: Menetrey, J. / Llinas, P.
History
DepositionSep 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin light chain 1
B: Kinesin light chain 1
C: Kinesin light chain 1
D: Kinesin light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3586
Polymers114,3094
Non-polymers492
Water00
1
A: Kinesin light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6022
Polymers28,5771
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin light chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6022
Polymers28,5771
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)28,5771
Polymers28,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)28,5771
Polymers28,5771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.490, 72.710, 110.870
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Kinesin light chain 1 / KLC 1


Mass: 28577.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLC1, KLC, KNS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07866
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% PEG8000, 0.6M magnesium acetate, 50mM sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.287→46.33 Å / Num. obs: 17338 / % possible obs: 98.6 % / Redundancy: 3.7 % / CC1/2: 0.991 / Net I/σ(I): 4.55
Reflection shellResolution: 3.287→3.48 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 2626 / CC1/2: 0.537

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ8

5oj8


Resolution: 3.287→46.33 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.467
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 867 5 %RANDOM
Rwork0.2014 ---
obs0.2037 17336 98.7 %-
Displacement parametersBiso max: 168.66 Å2 / Biso mean: 116.08 Å2 / Biso min: 62.05 Å2
Baniso -1Baniso -2Baniso -3
1-20.2538 Å20 Å2-5.5388 Å2
2---33.8247 Å20 Å2
3---13.5709 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 3.287→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 2 0 5987
Biso mean--72.01 --
Num. residues----827
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1939SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1093HARMONIC5
X-RAY DIFFRACTIONt_it6105HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion846SEMIHARMONIC5
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_contact4926SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6105HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8364HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion23.34
LS refinement shellResolution: 3.29→3.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 44
RfactorNum. reflection% reflection
Rfree0.311 20 4.95 %
Rwork0.3244 384 -
all0.3237 404 -
obs--69.11 %
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)
19.58180.65122.21180.90470.13952.38860.2221-0.5646-0.65130.1097-0.165-0.07670.2156-0.08-0.0571-0.2229-0.0675-0.0345-0.12080.0601-0.386613.141914.475527.6441
28.947-0.6419-1.98820.21560.77661.48740.07570.50930.6743-0.1189-0.11350.0244-0.214-0.20590.0379-0.32370.0241-0.00660.03370.0458-0.33817.652944.94727.7877
37.2583-0.2349-0.52211.035-0.04321.64330.05020.61210.0682-0.04520.0530.2953-0.212-0.4217-0.1031-0.33260.07950.04360.175-0.0253-0.433934.099518.9633-0.1315
49.35240.7665-0.07171.8096-0.02031.3553-0.0462-0.546-0.12950.1113-0.06260.42750.29-0.52750.1088-0.37830.02-0.11370.0688-0.209-0.428428.769740.385655.5369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A210 - 416
2X-RAY DIFFRACTION2{ B|* }B210 - 417
3X-RAY DIFFRACTION3{ C|* }C210 - 416
4X-RAY DIFFRACTION4{ D|* }D210 - 416

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