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- PDB-5gsz: Crystal Structure of the KIF19A Motor Domain Complexed with Mg-ADP -

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Basic information

Entry
Database: PDB / ID: 5gsz
TitleCrystal Structure of the KIF19A Motor Domain Complexed with Mg-ADP
ComponentsKinesin-like protein KIF19
KeywordsMOTOR PROTEIN / kinesin / motor domain / Mg-ADP
Function / homology
Function and homology information


axonemal microtubule depolymerization / plus-end specific microtubule depolymerization / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed microtubule motor activity / kinesin complex / microtubule-based movement / axoneme / cilium / microtubule binding ...axonemal microtubule depolymerization / plus-end specific microtubule depolymerization / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed microtubule motor activity / kinesin complex / microtubule-based movement / axoneme / cilium / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding
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 KIF19
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsWang, D. / Nitta, R. / Hirokawa, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan23000013 Japan
the Ministry of Education, Culture, Sports, Science and Technology of Japan15K08168 Japan
CitationJournal: Elife / Year: 2016
Title: Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A.
Authors: Doudou Wang / Ryo Nitta / Manatsu Morikawa / Hiroaki Yajima / Shigeyuki Inoue / Hideki Shigematsu / Masahide Kikkawa / Nobutaka Hirokawa /
Abstract: The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among ...The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among kinesins, KIF19A possesses the dual functions of motility along ciliary microtubules and depolymerization of microtubules. To elucidate the molecular mechanisms of these functions we solved the crystal structure of its motor domain and determined its cryo-electron microscopy structure complexed with a microtubule. The features of KIF19A that enable its dual function are clustered on its microtubule-binding side. Unexpectedly, a destabilized switch II coordinates with a destabilized L8 to enable KIF19A to adjust to both straight and curved microtubule protofilaments. The basic clusters of L2 and L12 tether the microtubule. The long L2 with a characteristic acidic-hydrophobic-basic sequence effectively stabilizes the curved conformation of microtubule ends. Hence, KIF19A utilizes multiple strategies to accomplish the dual functions of motility and microtubule depolymerization by ATP hydrolysis.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1213
Polymers39,6691
Non-polymers4522
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-16 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.604, 122.604, 56.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Kinesin-like protein KIF19 / Kinesin-8 motor / KIF19A


Mass: 39669.016 Da / Num. of mol.: 1 / Fragment: UNP residues 1-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif19, Kif19a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q99PT9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ethylene Glycol, PEG8000, Tris-Bicine, Magnesium chloride, Calcium chloride

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 12043 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.5
Reflection shellResolution: 2.71→2.81 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.995 / Rejects: 0 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→34.32 Å / SU ML: 0.45 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.302 574 4.78 %
Rwork0.222 11434 -
obs0.225 12008 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.91 Å2 / Biso mean: 57.1 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.72→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 40 28 2311
Biso mean--42.69 51.67 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7177-2.9910.37221430.261927912934
2.991-3.42350.31771500.245827812931
3.4235-4.31190.3081340.210828663000
4.3119-34.32580.27511470.212529963143

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