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- PDB-2zfk: Crystal Structure of the Kif1A Motor Domain during Mg release: Mg... -

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Basic information

Entry
Database: PDB / ID: 2zfk
TitleCrystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-2
ComponentsKinesin-like protein KIF1A, Kinesin heavy chain isoform 5C
KeywordsTRANSPORT PROTEIN / kinesin / Alpha and Beta Protein / Enzyme / ATPase / P-loop / Motor Protein / ATP-binding / Coiled coil / Microtubule / Nucleotide-binding
Function / homology
Function and homology information


distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde synaptic vesicle transport / neuronal dense core vesicle membrane / plus-end-directed kinesin ATPase / dense core granule cytoskeletal transport / Kinesins / anterograde axonal protein transport / regulation of dendritic spine development / apolipoprotein receptor binding ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde synaptic vesicle transport / neuronal dense core vesicle membrane / plus-end-directed kinesin ATPase / dense core granule cytoskeletal transport / Kinesins / anterograde axonal protein transport / regulation of dendritic spine development / apolipoprotein receptor binding / COPI-dependent Golgi-to-ER retrograde traffic / intracellular mRNA localization / ciliary rootlet / MHC class II antigen presentation / regulation of dendritic spine morphogenesis / motor neuron axon guidance / plus-end-directed microtubule motor activity / kinesin complex / microtubule motor activity / mRNA transport / neuronal dense core vesicle / postsynaptic cytosol / axonal growth cone / axon cytoplasm / dendrite cytoplasm / GABA-ergic synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / microtubule / neuron projection / neuronal cell body / synapse / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Kinesin motor domain / Kinesin ...: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Kinesin motor domain / Kinesin / Kinesin-like protein / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / PH domain / Kinesin motor domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin heavy chain isoform 5C / Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsNitta, R. / Okada, Y. / Hirokawa, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin.
Authors: Nitta, R. / Okada, Y. / Hirokawa, N.
History
DepositionJan 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 KIF1A, Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8245
Polymers41,1281
Non-polymers6964
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.477, 50.162, 157.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C / Axonal transporter of synaptic vesi cles / Kinesin heavy chain neuron-specifiC 2


Mass: 41128.215 Da / Num. of mol.: 1 / Fragment: KIF1A (residues 1-355), KIF5C (residues 329-334)
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN COMPRISES RESIDUES 1-355 OF Kinesin-like protein KIF1A, AND RESIDUES 329-334 OF Kinesin heavy chain isoform 5C, AND C-TERMINAL TAIL WITH SEQUENCE HHHHH
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: P33173, UniProt: P28738
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 3235

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Processing

Software
NameVersionClassification
CNS1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VFV

1vfv


Resolution: 3.61→14.99 Å / Rfactor Rfree error: 0.021 / Data cutoff high absF: 287001.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.349 264 9.9 %RANDOM
Rwork0.292 ---
obs0.292 2671 69.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.1994 Å2 / ksol: 0.09667957 e/Å3
Displacement parametersBiso mean: 74.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å20 Å20 Å2
2--57.38 Å20 Å2
3----64.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.65 Å
Luzzati d res low-15 Å
Luzzati sigma a0.6 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3.61→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 44 27 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.871.5
X-RAY DIFFRACTIONc_mcangle_it8.272
X-RAY DIFFRACTIONc_scbond_it5.62
X-RAY DIFFRACTIONc_scangle_it9.012.5
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.089 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.473 28 10.9 %
Rwork0.34 229 -
obs--42.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp.paramadp.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
X-RAY DIFFRACTION5trs.paramtrs.top

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