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- PDB-7eo9: Crystal structure of KIF1A Motor-Neck domain with ADP-Mg-AlFx -

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Basic information

Entry
Database: PDB / ID: 7eo9
TitleCrystal structure of KIF1A Motor-Neck domain with ADP-Mg-AlFx
ComponentsKinesin-like protein KIF1A
KeywordsMOTOR PROTEIN / kinesin
Function / homology
Function and homology information


protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / Kinesins / regulation of dendritic spine development / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport ...protein transport along microtubule / neuronal dense core vesicle membrane / interkinetic nuclear migration / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / Kinesins / regulation of dendritic spine development / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / plus-end-directed microtubule motor activity / kinesin complex / microtubule-based movement / neuronal dense core vesicle / axon cytoplasm / vesicle-mediated transport / synaptic vesicle / presynapse / microtubule binding / postsynapse / microtubule / neuron projection / axon / dendrite / neuronal cell body / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding
Similarity search - Function
: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / 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 / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsOgawa, T. / Jiang, X. / Hirokawa, N.
Funding support Japan, 5items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06372 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)20K07222 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)20K16483 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
CitationJournal: Embo J. / Year: 2022
Title: A neuropathy-associated kinesin KIF1A mutation hyper-stabilizes the motor-neck interaction during the ATPase cycle.
Authors: Morikawa, M. / Jerath, N.U. / Ogawa, T. / Morikawa, M. / Tanaka, Y. / Shy, M.E. / Zuchner, S. / Hirokawa, N.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5084
Polymers43,9721
Non-polymers5353
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-17 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.502, 57.319, 154.826
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 KIF1A / Axonal transporter of synaptic vesicles


Mass: 43972.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif1a, Atsv, Kif1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33173
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Ammonium acetate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. obs: 11987 / % possible obs: 96.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 39.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.063 / Net I/σ(I): 10.1
Reflection shellResolution: 2.57→2.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 859 / CC1/2: 0.898 / Rpim(I) all: 0.307 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VFX

1vfx


Resolution: 2.57→28.68 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.309 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.2 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 616 5.1 %RANDOM
Rwork0.2252 ---
obs0.2259 11371 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.86 Å2 / Biso mean: 48.26 Å2 / Biso min: 27.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20 Å2
2--8.39 Å2-0 Å2
3----5.36 Å2
Refinement stepCycle: final / Resolution: 2.57→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 32 24 2801
Biso mean--43.32 44.67 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132818
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172639
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6533811
X-RAY DIFFRACTIONr_angle_other_deg1.31.5856071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.655348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14322.237152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59115502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
LS refinement shellResolution: 2.57→2.637 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 39 -
Rwork0.308 859 -
obs--100 %

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