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- PDB-7eob: Crystal structure of KIF1A Motor-Neck domain E239K mutant with AD... -

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Basic information

Entry
Database: PDB / ID: 7eob
TitleCrystal structure of KIF1A Motor-Neck domain E239K mutant with ADP-Mg-AlFx
ComponentsKinesin-like protein KIF1A
KeywordsMOTOR PROTEIN / kinesin
Function / homology
Function and homology information


anterograde synaptic vesicle transport / protein transport along microtubule / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / Kinesins / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development ...anterograde synaptic vesicle transport / protein transport along microtubule / interkinetic nuclear migration / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / Kinesins / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / regulation of dendritic spine development / 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 / vesicle-mediated transport / axon cytoplasm / synaptic vesicle / presynapse / microtubule binding / microtubule / postsynapse / neuron projection / axon / neuronal cell body / dendrite / 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: 1.76 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5084
Polymers43,9731
Non-polymers5353
Water1,928107
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 area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.655, 57.249, 155.041
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: 43972.543 Da / Num. of mol.: 1 / Mutation: E239K
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-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#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.: 107 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
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: 1.76→30 Å / Num. obs: 36686 / % possible obs: 97.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.04 / Net I/σ(I): 13.4
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3095 / CC1/2: 0.805 / Rpim(I) all: 0.376 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EO9

7eo9


Resolution: 1.76→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1829 -RANDOM
Rwork0.215 ---
obs-36686 97.7 %-
Displacement parametersBiso max: 107.82 Å2 / Biso mean: 40.2319 Å2 / Biso min: 20.08 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 32 107 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132831
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172666
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6533826
X-RAY DIFFRACTIONr_angle_other_deg2.3171.5886134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99122.338154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50815506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9661522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023173
X-RAY DIFFRACTIONr_gen_planes_other0.010.02642
X-RAY DIFFRACTIONr_rigid_bond_restr5.57832830
LS refinement shellResolution: 1.763→1.808 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 108 -
Rwork0.338 2126 -
all-2234 -
obs--81.5 %
Refinement TLS params.Method: refined / Origin x: 18.8417 Å / Origin y: 3.311 Å / Origin z: 19.3472 Å
111213212223313233
T0.0061 Å2-0.0002 Å20.0003 Å2-0.0098 Å20.0001 Å2--0.0004 Å2
L0.0025 °2-0.0011 °2-0.0008 °2-0.0012 °20.0001 °2--0.0071 °2
S-0.0001 Å °-0.0003 Å °-0.0003 Å °0 Å °-0.0004 Å °0.0006 Å °0.0004 Å °0.0002 Å °0.0004 Å °

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