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- PDB-5lt2: nucleotide-free kinesin-1 motor domain, P1 crystal form -

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Basic information

Entry
Database: PDB / ID: 5lt2
Titlenucleotide-free kinesin-1 motor domain, P1 crystal form
ComponentsKinesin-like protein
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 / plus-end-directed microtubule motor activity / vesicle transport along microtubule / 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 / Kinesin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCao, L. / Gigant, B.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
ARC 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-like protein
B: Kinesin-like protein
C: Kinesin-like protein
D: Kinesin-like protein
E: Kinesin-like protein
K: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,71717
Polymers217,6606
Non-polymers1,05711
Water5,747319
1
A: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3732
Polymers36,2771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3732
Polymers36,2771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5654
Polymers36,2771
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5654
Polymers36,2771
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3732
Polymers36,2771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4693
Polymers36,2771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.740, 101.452, 101.588
Angle α, β, γ (deg.)119.24, 91.96, 91.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Kinesin-like protein / nucleotide-free kinesin-1 motor domain


Mass: 36276.746 Da / Num. of mol.: 6 / Mutation: C7S, C65A, C168A, C174S, C294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6P164, UniProt: P33176*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Mes pH 6.5 0.16 M 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: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→49 Å / Num. obs: 59440 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rrim(I) all: 0.23 / Net I/σ(I): 6.8
Reflection shellRrim(I) all: 1.61

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Processing

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

4lnu


Resolution: 2.6→38.401 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.6
RfactorNum. reflection% reflection
Rfree0.2488 2010 3.38 %
Rwork0.193 --
obs0.1949 59403 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13840 0 55 319 14214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114101
X-RAY DIFFRACTIONf_angle_d1.39119108
X-RAY DIFFRACTIONf_dihedral_angle_d14.4214976
X-RAY DIFFRACTIONf_chiral_restr0.0542217
X-RAY DIFFRACTIONf_plane_restr0.0072480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.33211420.27354082X-RAY DIFFRACTION98
2.665-2.73710.32631410.27284110X-RAY DIFFRACTION98
2.7371-2.81760.36551600.26444066X-RAY DIFFRACTION98
2.8176-2.90850.3381470.24894053X-RAY DIFFRACTION98
2.9085-3.01240.36451440.24524144X-RAY DIFFRACTION98
3.0124-3.1330.28911630.2254024X-RAY DIFFRACTION98
3.133-3.27550.26931330.22314193X-RAY DIFFRACTION98
3.2755-3.44810.29131430.20294055X-RAY DIFFRACTION98
3.4481-3.6640.25111450.17394170X-RAY DIFFRACTION99
3.664-3.94660.2471420.16974127X-RAY DIFFRACTION99
3.9466-4.34330.22721510.16184089X-RAY DIFFRACTION98
4.3433-4.97060.19951340.15474114X-RAY DIFFRACTION98
4.9706-6.25810.23131200.18974123X-RAY DIFFRACTION98
6.2581-38.40510.16651450.17154043X-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)
12.69760.16170.37851.72130.11591.18340.0331-0.4192-0.38120.16430.04630.0970.0924-0.0896-0.05340.29070.0286-0.0350.23950.04640.355312.64812.114111.0495
23.7528-0.2603-0.29362.6661-0.71681.78130.56140.9380.9625-0.0222-0.3704-0.163-0.22610.1953-0.1680.46620.0650.11960.53270.22040.554623.8497.721450.8696
33.17130.4234-0.82781.90630.07281.75510.1050.16060.5693-0.1686-0.04150.1378-0.1878-0.0591-0.01760.2955-0.0021-0.02210.20890.01670.338728.534452.34778.822
43.1149-0.65660.52921.8773-0.25792.51730.00720.4431-0.2245-0.15360.03680.12330.0796-0.1591-0.0240.2885-0.0294-0.01470.3144-0.02940.2493-2.57729.3682-25.7823
53.7018-0.0464-0.75431.01180.0782.22150.2253-0.86010.04440.2-0.1281-0.1796-0.0490.238-0.04530.3205-0.0738-0.05060.5054-0.05350.28031.079547.384138.8363
63.35041.30550.75222.42750.49521.23140.06540.2533-1.0538-0.0235-0.0006-0.40150.19110.1303-0.03060.3580.04410.00230.2556-0.07560.7356-14.5864-11.8875-7.6485
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 5 through 324)
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 325)
5X-RAY DIFFRACTION5(chain 'E' and resid 7 through 324)
6X-RAY DIFFRACTION6(chain 'K' and resid 5 through 324)

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