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- PDB-3lre: Crystal Structure Analysis of Human Kinesin-8 Motor Domain -

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Basic information

Entry
Database: PDB / ID: 3lre
TitleCrystal Structure Analysis of Human Kinesin-8 Motor Domain
ComponentsKinesin-like protein KIF18A
KeywordsMOTOR PROTEIN / nucleotide binding / microtubule binding / ATP-binding / Cell projection / Cytoskeleton / Glycoprotein / Microtubule / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule depolymerization ...tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule depolymerization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic metaphase chromosome alignment / seminiferous tubule development / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / regulation of microtubule cytoskeleton organization / Resolution of Sister Chromatid Cohesion / cellular response to estradiol stimulus / RHO GTPases Activate Formins / caveola / kinetochore / Separation of Sister Chromatids / protein transport / actin binding / microtubule cytoskeleton / microtubule binding / centrosome / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF18A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrejc, K. / Moores, C.A. / Hartman, J.
CitationJournal: EMBO J / Year: 2010
Title: Insight into the molecular mechanism of the multitasking kinesin-8 motor.
Authors: Carsten Peters / Katjuša Brejc / Lisa Belmont / Andrew J Bodey / Yan Lee / Ming Yu / Jun Guo / Roman Sakowicz / James Hartman / Carolyn A Moores /
Abstract: Members of the kinesin-8 motor class have the remarkable ability to both walk towards microtubule plus-ends and depolymerise these ends on arrival, thereby regulating microtubule length. To analyse ...Members of the kinesin-8 motor class have the remarkable ability to both walk towards microtubule plus-ends and depolymerise these ends on arrival, thereby regulating microtubule length. To analyse how kinesin-8 multitasks, we studied the structure and function of the kinesin-8 motor domain. We determined the first crystal structure of a kinesin-8 and used cryo-electron microscopy to calculate the structure of the microtubule-bound motor. Microtubule-bound kinesin-8 reveals a new conformation compared with the crystal structure, including a bent conformation of the α4 relay helix and ordering of functionally important loops. The kinesin-8 motor domain does not depolymerise stabilised microtubules with ATP but does form tubulin rings in the presence of a non-hydrolysable ATP analogue. This shows that, by collaborating, kinesin-8 motor domain molecules can release tubulin from microtubules, and that they have a similar mechanical effect on microtubule ends as kinesin-13, which enables depolymerisation. Our data reveal aspects of the molecular mechanism of kinesin-8 motors that contribute to their unique dual motile and depolymerising functions, which are adapted to control microtubule length.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF18A
B: Kinesin-like protein KIF18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4806
Polymers79,5772
Non-polymers9034
Water4,414245
1
A: Kinesin-like protein KIF18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2403
Polymers39,7881
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2403
Polymers39,7881
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Kinesin-like protein KIF18A
hetero molecules

B: Kinesin-like protein KIF18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4806
Polymers79,5772
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3730 Å2
ΔGint-41 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.420, 79.744, 140.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin-like protein KIF18A / Marrow stromal KIF18A / MS-KIF18A


Mass: 39788.254 Da / Num. of mol.: 2 / Fragment: UNP residues 1-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF18A, OK/SW-cl.108 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8NI77
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 275 K / Method: vapor diffusion / pH: 7.8
Details: 10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER AXS PROTEUM/R6000 / Detector: CCD / Date: Apr 12, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→70.71 Å / Num. obs: 39803 / % possible obs: 98.8 % / Rsym value: 0.064 / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
LSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T5C

1t5c


Resolution: 2.2→70.71 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.301 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.753 / SU B: 5.875 / SU ML: 0.151 / SU R Cruickshank DPI: 0.269 / SU Rfree: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1988 5 %RANDOM
Rwork0.221 ---
obs0.223 39755 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.66 Å2 / Biso mean: 33.274 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 56 245 4911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214737
X-RAY DIFFRACTIONr_bond_other_d0.0020.024282
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9646401
X-RAY DIFFRACTIONr_angle_other_deg0.92539987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985579
X-RAY DIFFRACTIONr_chiral_restr0.1990.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025140
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02899
X-RAY DIFFRACTIONr_nbd_refined0.2210.2961
X-RAY DIFFRACTIONr_nbd_other0.2430.24845
X-RAY DIFFRACTIONr_nbtor_other0.0870.22918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.215
X-RAY DIFFRACTIONr_mcbond_it1.0051.52918
X-RAY DIFFRACTIONr_mcangle_it1.87324710
X-RAY DIFFRACTIONr_scbond_it2.45431819
X-RAY DIFFRACTIONr_scangle_it4.1024.51691
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.33 122
Rwork0.245 2436
all-2558

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