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- PDB-1vfz: Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4 -

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Basic information

Entry
Database: PDB / ID: 1vfz
TitleCrystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4
ComponentsPROTEIN (Fusion protein consisting of Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C and A HIS TAG
KeywordsTRANSPORT PROTEIN / kinesin / microtubule / motor
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 / regulation of dendritic spine morphogenesis / MHC class II antigen presentation / 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 / VANADATE ION / Kinesin heavy chain isoform 5C / Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsNitta, R. / Kikkawa, M. / Okada, Y. / Hirokawa, N.
CitationJournal: Science / Year: 2004
Title: KIF1A Alternately Uses Two Loops to Bind Microtubules
Authors: Nitta, R. / Kikkawa, M. / Okada, Y. / Hirokawa, N.
History
DepositionApr 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 25, 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_ref_seq_dif / 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_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.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_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_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: PROTEIN (Fusion protein consisting of Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C and A HIS TAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6954
Polymers41,1281
Non-polymers5663
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.471, 51.805, 156.992
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 PROTEIN (Fusion protein consisting of Kinesin-like protein KIF1A, Kinesin heavy chain isoform 5C and A HIS TAG / Axonal transporter of synaptic vesicles


Mass: 41128.215 Da / Num. of mol.: 1
Fragment: Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C
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: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: P33173, UniProt: P28738
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Sodium acetate, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 17233 / Num. obs: 17147 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.2 Å2
Reflection shellResolution: 2.24→2.32 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I5S

1i5s


Resolution: 2.24→23.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 101547.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1609 10.1 %RANDOM
Rwork0.215 ---
all0.232 16986 --
obs0.215 16001 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1818 Å2 / ksol: 0.420953 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.51 Å20 Å20 Å2
2--17.47 Å20 Å2
3----9.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-24 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.24→23.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 33 174 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_mcangle_it4.212
X-RAY DIFFRACTIONc_scbond_it5.032
X-RAY DIFFRACTIONc_scangle_it6.552.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 246 9.9 %
Rwork0.26 2241 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.ADPTOPOLOGY.ADP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION5VO4.PARAMVO4.TOP

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