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- PDB-6fv0: Crystal structure of the TPR domain of KLC1 in complex with the C... -

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Basic information

Entry
Database: PDB / ID: 6fv0
TitleCrystal structure of the TPR domain of KLC1 in complex with the C-terminal peptide of torsinA
Components
  • Kinesin light chain 1,Torsin-1A
  • nanobodySingle-domain antibody
KeywordsMOTOR PROTEIN / Protein complex / nanobody / cargo recognition
Function / homology
Function and homology information


: / RHO GTPases activate KTN1 / nuclear membrane organization / extrinsic component of endoplasmic reticulum membrane / membrane-bounded organelle / organelle organization / Kinesins / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / COPI-dependent Golgi-to-ER retrograde traffic ...: / RHO GTPases activate KTN1 / nuclear membrane organization / extrinsic component of endoplasmic reticulum membrane / membrane-bounded organelle / organelle organization / Kinesins / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / COPI-dependent Golgi-to-ER retrograde traffic / intermediate filament cytoskeleton organization / protein deneddylation / regulation of protein localization to cell surface / Cargo recognition for clathrin-mediated endocytosis / protein localization to synapse / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / MHC class II antigen presentation / axo-dendritic transport / : / stress granule disassembly / ciliary rootlet / wound healing, spreading of cells / synaptic vesicle transport / kinesin complex / microtubule-based movement / chaperone cofactor-dependent protein refolding / kinesin binding / protein localization to nucleus / chaperone-mediated protein folding / cytoskeletal protein binding / tubulin binding / secretory granule / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / intracellular protein transport / cytoplasmic vesicle membrane / neuron projection development / unfolded protein binding / synaptic vesicle / nuclear envelope / growth cone / cytoplasmic vesicle / nuclear membrane / response to oxidative stress / vesicle / microtubule / cytoskeleton / cell adhesion / neuron projection / axon / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Torsin-1A / Torsin / Torsin 1/2 / Torsin / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat ...Torsin-1A / Torsin / Torsin 1/2 / Torsin / Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Kinesin light chain 1 / Kinesin light chain / Torsin-1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsPernigo, S. / Dodding, M.P. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006774/1 United Kingdom
Citation
Journal: Elife / Year: 2018
Title: Structural basis for isoform-specific kinesin-1 recognition of Y-acidic cargo adaptors.
Authors: Pernigo, S. / Chegkazi, M.S. / Yip, Y.Y. / Treacy, C. / Glorani, G. / Hansen, K. / Politis, A. / Bui, S. / Dodding, M.P. / Steiner, R.A.
#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
DepositionFeb 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Kinesin light chain 1,Torsin-1A
F: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9513
Polymers50,8452
Non-polymers1061
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, gel filtration, assay for oligomerization, fluorescence polarisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-3 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.040, 89.680, 50.990
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kinesin light chain 1,Torsin-1A / Dystonia 1 protein / Torsin ATPase 1 / Torsin family 1 member A


Mass: 37448.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain A is a fusion in a chimeric construct of TPR domain of KLC1 and the C-terminal peptide of torsinA via a (TGS)10 linker.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klc1, Kns2, Tor1a, Dyt1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q5UE59, UniProt: Q9ER39, UniProt: O88447*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Antibody nanobody / Single-domain antibody


Mass: 13395.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 30% propan-2-ol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→52.5 Å / Num. obs: 21275 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Net I/σ(I): 9
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1021 / CC1/2: 0.741 / Rpim(I) all: 0.52 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FUZ

6fuz


Resolution: 2.29→52.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1061 5.05 %RANDOM
Rwork0.208 ---
obs0.21 21016 98.4 %-
Displacement parametersBiso mean: 65.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.6985 Å20 Å2-9.6174 Å2
2---6.5911 Å20 Å2
3---5.8927 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.29→52.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 7 90 3136
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073100HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934183HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1103SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it3100HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion18.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
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_contact3490SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.305 134 4.99 %
Rwork0.262 2554 -
all0.264 2688 -
obs--94.5 %
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)
11.097-0.0114-1.70100.2951-0.4998-0.00470.0352-0.0437-0.0035-0.0233-0.03740.06290.06790.028-0.3441-0.23050.01350.3772-0.14230.029447.79280.49572.2689
2-0.01870.57011.56710.33131.25151.8566-0.01840.01410.0894-0.01270.0398-0.0125-0.005-0.0043-0.0214-0.2111-0.26250.10540.5938-0.3046-0.204745.051312.82911.844
30.6098-0.1342.04520.5444-3.53651.244-0.0133-0.28490.0554-0.00340.0049-0.11130.02810.19560.0084-0.6065-0.06120.01160.45390.2903-0.1349.90167.5979-7.1242
43.5197-4.0224-3.29061.2131-0.59650.7966-0.0326-0.00690.00780.17830.0115-0.13590.08410.06010.0211-0.00750.21070.26390.1850.31540.32750.3269-4.5229-12.4779
51.50343.867-1.61394.7357-2.08286.3767-0.1346-0.40.0488-0.1367-0.1882-0.2163-0.20750.33180.3228-0.26180.01210.07650.07290.2064-0.113440.58454.2404-6.7092
60.39440.4547-0.59161.389-3.43891.6190.00370.17960.268-0.1022-0.07830.0704-0.03360.07280.0746-0.1368-0.08130.06370.15910.2009-0.010735.848711.2383-12.3416
70.4653-2.07722.40584.8609-2.81551.3249-0.05620.3069-0.4847-0.4488-0.1454-0.0410.34610.20360.20160.07240.11580.3106-0.00620.04770.111436.302-7.5731-10.798
81.3466-2.11270.55112.8854-2.47745.9845-0.13630.9343-0.0956-0.4593-0.1262-0.1570.0745-0.19260.2625-0.0565-0.06870.08590.0199-0.0021-0.0925.3093.0832-9.4996
91.12692.2921-3.38771.1610.6152-0.32850.0476-0.0176-0.57810.1556-0.0610.14540.25050.02820.01340.0597-0.05580.2163-0.03770.02770.1525.2085-10.5775-2.9701
107.0759-0.3408-2.49740.66-0.11612.3922-0.18730.006-0.6005-0.2661-0.30770.0240.30860.06370.495-0.0954-0.03580.0909-0.07950.0504-0.133421.1734-1.04780.544
114.0954-1.223-4.61582.9366-3.4173.4922-0.0748-0.0299-0.2497-0.1504-0.10950.2490.1475-0.42890.1843-0.0402-0.01050.0420.00520.0034-0.033413.9686-1.11283.5053
124.7646-1.0187-3.02543.5922-2.9560.80610.0316-0.75080.04750.0006-0.3834-0.2111-0.19760.63690.3518-0.0861-0.0871-0.04280.23750.1242-0.138923.39222.868911.6012
134.02212.3643-2.365.1260.7840.94740.3238-0.10180.2020.0546-0.42670.3598-0.68280.27820.103-0.0458-0.10360.0492-0.07290.0207-0.108611.7911.509110.9806
14-0.46681.75143.15791.0665-2.29953.4972-0.04510.01520.07870.12570.0233-0.1458-0.01970.18650.0218-0.1142-0.2499-0.12630.51230.07-0.161523.800911.068826.4991
154.3465-0.28060.75650.1847-3.35180.6162-0.0425-0.14170.09010.18940.1389-0.13220.06520.1547-0.09640.1562-0.30240.09390.1078-0.0327-0.262816.201317.993927.0876
160.34520.7591-1.13334.8404-3.09693.2099-0.0171-0.12240.10670.0293-0.1445-0.1337-0.04160.10460.16170.2564-0.28430.12920.1318-0.1429-0.052415.564922.449621.2145
17-0.04071.12770.49550.70710.03740.97830.0070.02760.09530.0167-0.005-0.1202-0.0775-0.0142-0.002-0.1422-0.33120.06780.28640.2095-0.20922.418918.345712.0209
18-0.07570.15180.2170.3879-0.56120.79220.00160.00540.1053-0.0123-0.10270.0403-0.1027-0.00790.101-0.0686-0.22930.1711-0.2146-0.1111-0.134713.336620.36612.4594
191.596-4.5188-0.07343.5364-1.47230.17910.01720.05720.0711-0.0611-0.07590.0062-0.1697-0.05330.05870.0354-0.24410.2801-0.1591-0.11630.25849.348926.033214.3784
200.20483.27220.29820.22742.45460.65220.01460.07880.0079-0.0295-0.088-0.1204-0.0330.1820.0733-0.0671-0.30530.1139-0.04930.03920.243624.537125.606116.4047
210.2947-0.99130.91860.00041.69881.2241-0.0081-0.06880.0540.2520.0732-0.26780.04490.2665-0.0651-0.15770.05550.08830.1880.2713-0.059415.7127-13.374126.3352
22-1.04762.24423.57630.4367-4.59852.1458-0.0131-0.0215-0.2182-0.0736-0.13070.01260.15850.05330.14380.07780.02810.1829-0.063-0.0630.1299-5.1436-19.941721.0523
231.67482.234-3.7030.0438-1.1441.0466-0.0386-0.11810.07050.080.0168-0.12280.24520.12820.0218-0.1728-0.00230.0793-0.13630.0545-0.12850.3629-12.397824.0045
241.1626-2.01381.17670.2938-1.03833.02640.0170.044-0.020.0492-0.0571-0.0476-0.07620.18290.0401-0.16860.067-0.00850.48320.2138-0.086418.2454-6.983927.1958
250.3183-1.3505-1.27520.38490.10822.0290.0769-0.0434-0.04560.1511-0.0986-0.2088-0.04930.08740.0217-0.1815-0.1866-0.02540.26560.1774-0.238617.4173-0.521920.9763
264.03232.4695-0.20910-3.2857-0.1384-0.0898-0.0069-0.3512-0.1981-0.20640.01460.37130.61250.2963-0.21370.05230.1354-0.06740.077-0.07610.198-12.515515.1725
271.8396-1.19410.27361.07430.57473.99550.02750.0399-0.1544-0.0222-0.06720.05420.050.03130.03960.34250.05140.2992-0.1384-0.00480.35868.789-21.46029.0691
282.01360.0747-0.30930.0549-2.04580.8845-0.0162-0.0745-0.27650.338-0.1949-0.2294-0.16820.24040.2111-0.1172-0.05680.09960.03820.0478-0.11199.9286-3.984614.6046
290.47392.3856-0.95112.4312-4.16180.8392-0.07310.059-0.11450.1782-0.07710.0901-0.0402-0.11470.1501-0.10560.02590.0650.1340.017-0.01956.86960.718814.2549
300.6494-0.3564-0.04411.10470.7999-0.0246-0.03790.08070.0176-0.0950.06120.0463-0.0041-0.0965-0.02330.07-0.03870.0330.0458-0.0428-0.01131.1557-8.168.0771
311.23761.8484-1.11530.02333.22481.68580.0161-0.121-0.1179-0.26420.07690.26760.0642-0.0753-0.093-0.07850.0112-0.0219-0.04590.0296-0.02380.1051-6.490816.6489
32-0.09921.3270.31331.1468-0.60080.56580.0241-0.19-0.01930.1834-0.0750.03930.04620.00070.05090.0792-0.14820.00440.20580.1141-0.123310.6659-1.026228.7198
330.3218-2.462-1.233502.3451.64620.0828-0.1907-0.0660.2646-0.11010.0946-0.16810.19010.0273-0.0846-0.00450.03890.1560.0372-0.13398.4213-6.184425.6094
341.19151.35290.48813.3190.11311.14050.01310.1902-0.37830.0491-0.0667-0.09630.1294-0.07130.0536-0.14390.02650.1168-0.0107-0.1488-0.0134-3.9835-13.202816.5194
352.00221.3166-1.70971.3062-1.66781.4505-0.0672-0.1036-0.1603-0.1633-0.14880.06080.25930.25340.21610.00350.08040.28-0.2285-0.09430.19743.4015-18.417114.7873
361.14521.2022-1.62051.4873-2.0336-0.4781-0.0322-0.2237-0.08830.1063-0.0135-0.05230.12740.06990.0457-0.12730.05750.19870.2080.1219-0.03915.2853-11.365516.2725
371.4121-2.0410.08380.0051-5.2168-0.0043-0.0099-0.0527-0.0074-0.05390.019-0.0728-0.08090.0879-0.0091-0.09890.14230.08310.34240.3080.149419.4018-14.035717.4771
380.7264-3.6173-2.97145.7489-0.49855.511-0.02820.0267-0.2681-0.103-0.2104-0.01050.3909-0.02470.23860.02470.12540.2756-0.19460.12040.11172.388-21.953720.0214
390.7851.2539-1.48821.0546-0.96090.18030.02490.0643-0.05870.03280.0033-0.0655-0.00180.0594-0.02820.12540.04590.07010.1910.20160.245617.959818.57742.7819
403.91794.47831.23482.03680.73150.4143-0.001-0.161-0.08440.0906-0.089-0.31620.07290.13720.0899-0.2611-0.06670.0699-0.01090.1036-0.258527.26756.03970.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|214 - A|220 }
2X-RAY DIFFRACTION2{ A|221 - A|230 }
3X-RAY DIFFRACTION3{ A|231 - A|240 }
4X-RAY DIFFRACTION4{ A|241 - A|252 }
5X-RAY DIFFRACTION5{ A|253 - A|267 }
6X-RAY DIFFRACTION6{ A|268 - A|276 }
7X-RAY DIFFRACTION7{ A|277 - A|296 }
8X-RAY DIFFRACTION8{ A|297 - A|320 }
9X-RAY DIFFRACTION9{ A|321 - A|332 }
10X-RAY DIFFRACTION10{ A|333 - A|353 }
11X-RAY DIFFRACTION11{ A|354 - A|368 }
12X-RAY DIFFRACTION12{ A|369 - A|389 }
13X-RAY DIFFRACTION13{ A|390 - A|409 }
14X-RAY DIFFRACTION14{ A|410 - A|420 }
15X-RAY DIFFRACTION15{ A|421 - A|431 }
16X-RAY DIFFRACTION16{ A|432 - A|462 }
17X-RAY DIFFRACTION17{ A|463 - A|468 }
18X-RAY DIFFRACTION18{ A|469 - A|474 }
19X-RAY DIFFRACTION19{ A|475 - A|483 }
20X-RAY DIFFRACTION20{ A|484 - A|495 }
21X-RAY DIFFRACTION21{ F|2 - F|7 }
22X-RAY DIFFRACTION22{ F|8 - F|15 }
23X-RAY DIFFRACTION23{ F|16 - F|21 }
24X-RAY DIFFRACTION24{ F|22 - F|28 }
25X-RAY DIFFRACTION25{ F|29 - F|33 }
26X-RAY DIFFRACTION26{ F|34 - F|40 }
27X-RAY DIFFRACTION27{ F|41 - F|46 }
28X-RAY DIFFRACTION28{ F|47 - F|53 }
29X-RAY DIFFRACTION29{ F|54 - F|60 }
30X-RAY DIFFRACTION30{ F|61 - F|65 }
31X-RAY DIFFRACTION31{ F|66 - F|71 }
32X-RAY DIFFRACTION32{ F|72 - F|76 }
33X-RAY DIFFRACTION33{ F|77 - F|81 }
34X-RAY DIFFRACTION34{ F|82 - F|88 }
35X-RAY DIFFRACTION35{ F|89 - F|94 }
36X-RAY DIFFRACTION36{ F|95 - F|100 }
37X-RAY DIFFRACTION37{ F|101 - F|106 }
38X-RAY DIFFRACTION38{ F|107 - F|115 }
39X-RAY DIFFRACTION39{ A|702 - A|706 }
40X-RAY DIFFRACTION40{ A|707 - A|712 }

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