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- PDB-5lt3: nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form -

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Basic information

Entry
Database: PDB / ID: 5lt3
Titlenucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form
ComponentsKinesin-1 heavy chain
KeywordsMOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / vesicle transport along microtubule / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / stress granule disassembly / natural killer cell mediated cytotoxicity / Insulin processing / synaptic vesicle transport / postsynaptic cytosol / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / axon guidance / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / centriolar satellite / Signaling by ALK fusions and activated point mutants / nuclear membrane / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinesin-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsCao, L. / Gigant, B.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Sci Rep / Year: 2017
Title: The structural switch of nucleotide-free kinesin.
Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

Downloads & links

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Assembly

Deposited unit
A: Kinesin-1 heavy chain
B: Kinesin-1 heavy chain
C: Kinesin-1 heavy chain
D: Kinesin-1 heavy chain
E: Kinesin-1 heavy chain
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,24914
Polymers217,4806
Non-polymers7698
Water3,603200
1
A: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2471
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2471
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2471
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5354
Polymers36,2471
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2471
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3432
Polymers36,2471
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.672, 101.299, 101.527
Angle α, β, γ (deg.)119.57, 91.91, 91.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 36246.719 Da / Num. of mol.: 6 / Mutation: C7S, C65A, T87A, C168A, C174S, C294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P33176
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Mes pH 6.5 0.2M ammonium sulfate 30% mPEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→48.9 Å / Num. obs: 59275 / % possible obs: 97.3 % / Redundancy: 2.9 % / CC1/2: 0.967 / Net I/σ(I): 3.8
Reflection shellHighest resolution: 2.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LNU

4lnu


Resolution: 2.59→33.176 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 2915 4.92 %
Rwork0.2031 --
obs0.2061 59275 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→33.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13757 0 40 200 13997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914013
X-RAY DIFFRACTIONf_angle_d1.36918976
X-RAY DIFFRACTIONf_dihedral_angle_d14.2674966
X-RAY DIFFRACTIONf_chiral_restr0.0542187
X-RAY DIFFRACTIONf_plane_restr0.0072468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5896-2.6320.34651040.30832251X-RAY DIFFRACTION82
2.632-2.67740.3651460.2862771X-RAY DIFFRACTION98
2.6774-2.7260.31251280.28292693X-RAY DIFFRACTION98
2.726-2.77840.32551380.24972615X-RAY DIFFRACTION97
2.7784-2.83510.30351300.24722777X-RAY DIFFRACTION98
2.8351-2.89670.31711450.24452649X-RAY DIFFRACTION97
2.8967-2.96410.32851260.24572694X-RAY DIFFRACTION98
2.9641-3.03820.32471430.24032699X-RAY DIFFRACTION98
3.0382-3.12020.30341400.22982692X-RAY DIFFRACTION98
3.1202-3.2120.29491360.23232738X-RAY DIFFRACTION98
3.212-3.31560.29291530.21452711X-RAY DIFFRACTION98
3.3156-3.4340.2851330.21252678X-RAY DIFFRACTION98
3.434-3.57130.24391280.19752760X-RAY DIFFRACTION98
3.5713-3.73360.28511560.19222699X-RAY DIFFRACTION98
3.7336-3.93020.25621460.17842728X-RAY DIFFRACTION98
3.9302-4.1760.2031480.17272671X-RAY DIFFRACTION98
4.176-4.49770.19511210.15582714X-RAY DIFFRACTION98
4.4977-4.9490.19471570.16232695X-RAY DIFFRACTION98
4.949-5.6620.25441470.19062762X-RAY DIFFRACTION99
5.662-7.12190.28741430.21212705X-RAY DIFFRACTION99
7.1219-33.17830.24421470.18512658X-RAY DIFFRACTION97
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)
12.57880.15550.4951.16870.23871.18850.0986-0.02-0.4697-0.0062-0.0147-0.12420.16470.0709-0.02710.277-0.0003-0.00290.18930.01590.2346-12.9533-3.0996-15.7252
23.5222-0.1579-0.52252.5579-0.7121.37120.37150.43441.0664-0.141-0.18440.1152-0.1443-0.0882-0.07610.36470.04090.08330.22260.07960.5723-23.5911-40.3018-31.9118
32.4734-0.750.21881.85390.02161.03140.07050.24280.3122-0.0616-0.0694-0.0793-0.12080.1965-0.01810.253-0.0160.00720.29460.0520.1702-28.808818.9001-49.776
42.45221.1115-0.53281.73560.05821.19070.0623-0.33110.07320.0593-0.0126-0.2106-0.01610.1104-0.03230.27940.0127-0.00650.2172-0.03530.2932.838737.3374-13.1539
53.054-0.8426-0.63211.7970.61041.62770.23950.575-0.911-0.0175-0.22060.30770.0834-0.2434-0.13690.25470.0272-0.09310.4063-0.14590.3821-1.1778-8.9963-60.2828
62.85210.10511.18780.9586-0.20881.88780.1823-0.8893-0.19130.2202-0.03740.169-0.0065-0.3345-0.08510.3707-0.04290.02140.550.07440.220314.251.632314.3018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 324)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 324)
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 324)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 324)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 324)
6X-RAY DIFFRACTION6(chain 'K' and resid 6 through 324)

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