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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 / ciliary rootlet / lysosome localization / MHC class II antigen presentation / axo-dendritic transport / kinesin complex / microtubule-based movement / natural killer cell mediated cytotoxicity ...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 / natural killer cell mediated cytotoxicity / Golgi organization / kinesin binding / regulation of protein localization / microtubule / neuron projection / endosome membrane / lysosomal membrane / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / PLEKHM2 PH domain-like / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / RUN / RUN domain / RUN domain superfamily / RUN domain ...: / : / PLEKHM2 PH domain-like / 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 / PH domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / PH-like domain superfamily / Tetratricopeptide-like helical 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
Revision 1.3Nov 13, 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
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
Has protein modificationY
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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