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- PDB-8bjs: Apo KIF20A[55-510] crystal structure -

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Basic information

Entry
Database: PDB / ID: 8bjs
TitleApo KIF20A[55-510] crystal structure
Components
  • Kinesin-like protein KIF20A
  • UNK-UNK-UNK-UNK
KeywordsMOTOR PROTEIN / Kinesin 6 / motor domain / ATPase / mitosis / cytokinesis / Golgi / microtubule
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / microtubule motor activity / microtubule-based movement / intercellular bridge / mitotic cytokinesis ...Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / microtubule motor activity / microtubule-based movement / intercellular bridge / mitotic cytokinesis / regulation of cytokinesis / spindle / protein transport / midbody / microtubule binding / microtubule / protein kinase binding / Golgi apparatus / nucleoplasm / ATP binding
Similarity search - Function
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
Similarity search - Domain/homology
Kinesin-like protein KIF20A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsRanaivoson, F.M. / Kikuti, C. / Crozet, V. / Sirkia, M.E. / Houdusse, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE13-0017-01 France
Foundation for Medical Research (France)DCM20181039553 France
CitationJournal: Open Biol / Year: 2023
Title: Nucleotide-free structures of KIF20A illuminate atypical mechanochemistry in this kinesin-6.
Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B ...Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B Asenjo / Hernando Sosa / Christoph F Schmidt / Steven S Rosenfeld / Anne Houdusse /
Abstract: KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the ...KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the nucleotide- and microtubule-binding sites of this kinesin-6 has been reported, but little is known about how its divergent sequence leads to atypical motility properties. We present here the first high-resolution structure of its motor domain that delineates the highly unusual structural features of this motor, including a long L6 insertion that integrates into the core of the motor domain and that drastically affects allostery and ATPase activity. Together with the high-resolution cryo-electron microscopy microtubule-bound KIF20A structure that reveals the microtubule-binding interface, we dissect the peculiarities of the KIF20A sequence that influence its mechanochemistry, leading to low motility compared to other kinesins. Structural and functional insights from the KIF20A pre-power stroke conformation highlight the role of extended insertions in shaping the motor's mechanochemical cycle. Essential for force production and processivity is the length of the neck linker in kinesins. We highlight here the role of the sequence preceding the neck linker in controlling its backward docking and show that a neck linker four times longer than that in kinesin-1 is required for the activity of this motor.
History
DepositionNov 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF20A
U: UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9053
Polymers52,8092
Non-polymers961
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.438, 48.490, 85.836
Angle α, β, γ (deg.)90.000, 124.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kinesin-like protein KIF20A / Kinesin-like protein 174 / Rab6-interacting kinesin-like protein / Rabkinesin-6


Mass: 52450.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli (E. coli) / References: UniProt: P97329
#2: Protein/peptide UNK-UNK-UNK-UNK


Mass: 358.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.8 M NaCl, 0.5 M (NH4)2SO4, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.73→64.24 Å / Num. obs: 12169 / % possible obs: 99.85 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1332 / Rrim(I) all: 0.1441 / Net I/σ(I): 9.5
Reflection shellResolution: 2.73→2.83 Å / Rmerge(I) obs: 0.6778 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 1209 / CC1/2: 0.887 / Rrim(I) all: 0.7307

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-SAD Structure

Resolution: 2.73→54.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.868 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1218 10.01 %RANDOM
Rwork0.206 ---
obs0.21 12169 100 %-
Displacement parametersBiso max: 140.72 Å2 / Biso mean: 64.12 Å2 / Biso min: 29.17 Å2
Baniso -1Baniso -2Baniso -3
1--11.2457 Å20 Å213.8501 Å2
2--0.5115 Å20 Å2
3---10.7343 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.73→54.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 5 46 2792
Biso mean--102.68 55.09 -
Num. residues----347
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d978SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it2803HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
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_contact3035SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2803HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3789HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion20.15
LS refinement shellResolution: 2.73→2.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3128 24 9.84 %
Rwork0.2404 220 -
all0.2471 244 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.0171 Å / Origin y: 3.7574 Å / Origin z: 17.5763 Å
111213212223313233
T-0.1184 Å20.0551 Å20.0518 Å2--0.128 Å20.0721 Å2---0.1049 Å2
L2.151 °20.1165 °21.9946 °2-0.8651 °20.1801 °2--3.8453 °2
S-0.0842 Å °-0.2505 Å °-0.0023 Å °0.1135 Å °0.1434 Å °0.1474 Å °-0.235 Å °-0.5702 Å °-0.0592 Å °
Refinement TLS groupSelection details: { A|* }

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