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- PDB-3zfw: Crystal structure of the TPR domain of kinesin light chain 2 in c... -

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Basic information

Entry
Database: PDB / ID: 3zfw
TitleCrystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide
Components
  • KINESIN LIGHT CHAIN 2
  • PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2
KeywordsHYDROLASE / KINESIN-CARGO RECOGNITION / MOTOR PROTEIN / TPR DOMAIN / SALMONELLA
Function / homology
Function and homology information


RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / lysosome localization / MHC class II antigen presentation / natural killer cell mediated cytotoxicity / axo-dendritic transport / ciliary rootlet / kinesin complex / microtubule-based movement ...RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / lysosome localization / MHC class II antigen presentation / natural killer cell mediated cytotoxicity / axo-dendritic transport / ciliary rootlet / kinesin complex / microtubule-based movement / Golgi organization / kinesin binding / regulation of protein localization / microtubule / endosome membrane / neuron projection / lysosomal membrane / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Tetratricopeptide repeat ...: / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / PH domain / Tetratricopeptide repeats / Tetratricopeptide repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Kinesin light chain 2 / Pleckstrin homology domain-containing family M member 2 / Kinesin light chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPernigo, S. / Lamprecht, A. / Steiner, R.A. / Dodding, M.P.
CitationJournal: Science / Year: 2013
Title: Structural Basis for Kinesin-1:Cargo Recognition.
Authors: Pernigo, S. / Lamprecht, A. / Steiner, R.A. / Dodding, M.P.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: 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

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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
X: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2
Y: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2


Theoretical massNumber of molelcules
Total (without water)69,1564
Polymers69,1564
Non-polymers00
Water00
1
A: KINESIN LIGHT CHAIN 2
X: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2


Theoretical massNumber of molelcules
Total (without water)34,5782
Polymers34,5782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area12170 Å2
MethodPISA
2
B: KINESIN LIGHT CHAIN 2
Y: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2


Theoretical massNumber of molelcules
Total (without water)34,5782
Polymers34,5782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-6.8 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.810, 90.860, 94.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1777, 0.9841, -0.000756), (0.9841, -0.1777, 0.000105), (-1)-40.5, 48.13, 93.09
2given(0.1997, 0.9798, -0.01407), (0.9798, -0.1994, 0.0165), (0.01336, -0.01708, -0.9998)-39.26, 48.07, 93.69

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Components

#1: Protein KINESIN LIGHT CHAIN 2 / KLC 2


Mass: 29861.936 Da / Num. of mol.: 2 / Fragment: TPR DOMAIN, RESIDUES 218-477
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 PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2 / PH DOMAIN-CONTAINING FAMILY M MEMBER 2 / SALMONELLA-INDUCED FILAMENTS A AND KINESIN-INTERACTING ...PH DOMAIN-CONTAINING FAMILY M MEMBER 2 / SALMONELLA-INDUCED FILAMENTS A AND KINESIN-INTERACTING PROTEIN / SIFA AND KINESIN-INTERACTING PROTEIN


Mass: 4716.028 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MOL ID 1 AND MOL ID 2 ARE EXPRESSED AS A SINGLE ENTITY. IT IS UNCLEAR WHICH OF CHAIN A OR B ARE JOINED TO CHAINS X OR Y.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IWE5
Sequence detailsRESIDUES MGSSHHHHHHSSGLVPRGSHM AND TGSTGSTGSTGSHM ARE DERIVED FROM THE CLONING STRATEGY. ONLY ...RESIDUES MGSSHHHHHHSSGLVPRGSHM AND TGSTGSTGSTGSHM ARE DERIVED FROM THE CLONING STRATEGY. ONLY RESIDUES TNLEWDDSAI BELONG TO Q8IWE5

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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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→54.42 Å / Num. obs: 17034 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 95.38 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 5.04 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CEQ

3ceq


Resolution: 2.9→52.42 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9264 / SU R Cruickshank DPI: 0.8 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.784 / SU Rfree Blow DPI: 0.327 / SU Rfree Cruickshank DPI: 0.334
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 854 5.01 %RANDOM
Rwork0.2022 ---
obs0.2042 17030 98.67 %-
Displacement parametersBiso mean: 108.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.0082 Å20 Å20 Å2
2---9.0697 Å20 Å2
3---9.0615 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 2.9→52.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 0 0 3749
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093813HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035144HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1382SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes541HARMONIC5
X-RAY DIFFRACTIONt_it3813HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion21.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
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_contact4211SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3128 164 6.11 %
Rwork0.275 2519 -
all0.2772 2683 -
obs--98.67 %
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)
10.55070.7164-1.44210.4941-0.90592.9171-0.01060.0599-0.03030.0148-0.02640.26420.1062-0.10260.0370.36320.035-0.18910.5415-0.0602-0.306-40.287417.322750.0863
25.86593.58521.47051.94671.960711.1992-0.01350.4237-0.0085-0.23910.2312-0.015-0.22070.1745-0.21770.52130.04960.00330.40680.0942-0.5876-29.73517.382753.4302
31.3192-4.08573.02463.7975-0.657910.8119-0.02880.14650.1594-0.41560.1630.0685-0.4804-0.1281-0.13420.23160.16080.01630.51240.1433-0.4111-31.673722.002961.8485
40.01631.49225.60366.4804-1.12966.1492-0.0158-0.02710.1377-0.1290.1218-0.0961-0.1893-0.1405-0.1060.55780.2508-0.0740.33360.2103-0.304-33.341826.632968.8142
55.9977-5.4581-2.56073.2813-0.900913.6941-0.1050.84220.0782-0.51870.0635-0.0269-0.6638-0.65110.0414-0.02110.0576-0.01840.02090.0335-0.1883-32.072919.464178.6929
65.0575-1.40212.86375.71960.54649.357-0.0271-0.3526-0.7182-0.12050.09140.38161.0424-0.3037-0.0643-0.0850.02830.0085-0.0964-0.03710.0115-27.48445.119692.1601
70.9195-5.5682-0.20896.0730.77420.2193-0.0503-0.0261-0.1925-0.1140.02680.11310.1554-0.07130.02350.4597-0.0715-0.1730.23950.11750.5561-25.2999-5.557390.3851
81.0585-2.1512-4.45574.4137-2.59772.16270.01760.2135-0.1429-0.0708-0.1676-0.4933-0.11360.33070.150.02140.05580.0113-0.1642-0.18460.0532-19.8052.347488.3405
910.6053-5.2826-5.5539.25971.78034.9743-0.0397-0.20150.335-0.25860.0465-0.25390.33690.4665-0.0068-0.05550.1707-0.0682-0.2528-0.05430.0788-16.8604-2.886791.4139
106.2662-1.6304-2.8760.13592.824712.77030.0648-0.2799-0.05350.15640.00650.0544-0.1163-0.1027-0.07130.28030.2449-0.07990.56690.0559-0.5385-31.842615.566840.7294
115.5534-5.3824-5.14744.7863-0.780510.14330.1175-0.372-0.36990.0135-0.1559-0.43740.05940.48730.03840.43580.304-0.18110.40410.1307-0.5366-24.00679.272335.1859
123.6129-5.1963-0.4361.5924-3.23318.93780.0619-0.56170.0360.1868-0.178-0.155-0.21680.60540.11620.20190.241-0.09370.55820.0771-0.3229-21.182314.653825.895
133.207-4.4780.40188.75040.137113.3758-0.1296-0.70030.00660.72230.0231-0.12730.29460.62520.1065-0.12350.1243-0.01920.11690.029-0.2874-25.585514.744714.7947
146.3357-4.51510.96652.4681-4.493211.6809-0.0592-0.4406-0.06660.15560.29940.12170.2216-0.2456-0.24010.01870.03180.0810.1068-0.0088-0.0848-33.728617.12569.164
158.6556-2.2263-2.98664.3007-1.95958.8866-0.1230.5162-0.4909-0.2866-0.08960.72160.2057-0.69020.2126-0.0732-0.0439-0.0143-0.178-0.04380.1305-42.889219.8325-2.4837
167.9042-3.65242.00922.62062.24790.380.028-0.1662-0.0382-0.0533-0.12720.06320.0704-0.18330.09920.15570.215-0.22470.44770.0360.531-50.350827.4487-3.7739
1713.3477-5.28832.83019.4846-1.81546.9357-0.0722-0.18210.76780.5261-0.0020.0451-0.3179-0.01140.0742-0.1804-0.0426-0.0088-0.3723-0.06090.1492-41.699329.74752.8224
182.6101-1.82071.37141.16135.15976.26080.01480.08960.10690.1170.0113-0.0271-0.25950.0807-0.0262-0.1860.0358-0.0969-0.2168-0.24030.3887-49.349631.04313.5278
190.86561.4886-5.72965.99531.61838.3155-0.00830.0494-0.0471-0.10590.13810.02340.1765-0.0463-0.12980.31920.0555-0.07770.43830.0263-0.4399-32.795513.01264.2999
205.30150.70553.903803.7955.0765-0.0075-0.0496-0.0389-0.06290.08230.1102-0.0092-0.0051-0.07480.44130.2550.1330.48170.0551-0.3874-33.086814.664128.3493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 236 -244
2X-RAY DIFFRACTION2CHAIN A AND RESID 245 - 272
3X-RAY DIFFRACTION3CHAIN A AND RESID 273 - 298
4X-RAY DIFFRACTION4CHAIN A AND RESID 299 - 315
5X-RAY DIFFRACTION5CHAIN A AND RESID 316 - 360
6X-RAY DIFFRACTION6CHAIN A AND RESID 361 - 419
7X-RAY DIFFRACTION7CHAIN A AND RESID 420 - 446
8X-RAY DIFFRACTION8CHAIN A AND RESID 447 - 460
9X-RAY DIFFRACTION9CHAIN A AND RESID 461 - 479
10X-RAY DIFFRACTION10CHAIN B AND RESID 236 - 258
11X-RAY DIFFRACTION11CHAIN B AND RESID 259 - 291
12X-RAY DIFFRACTION12CHAIN B AND RESID 292 - 316
13X-RAY DIFFRACTION13CHAIN B AND RESID 317 - 355
14X-RAY DIFFRACTION14CHAIN B AND RESID 356 - 380
15X-RAY DIFFRACTION15CHAIN B AND RESID 381 - 417
16X-RAY DIFFRACTION16CHAIN B AND RESID 418 - 443
17X-RAY DIFFRACTION17CHAIN B AND RESID 444 - 468
18X-RAY DIFFRACTION18CHAIN B AND RESID 469 - 477
19X-RAY DIFFRACTION19CHAIN X AND RESID 203 - 213
20X-RAY DIFFRACTION20CHAIN Y AND RESID 203 - 212

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