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- PDB-2hxh: KIF1A head-microtubule complex structure in adp-form -

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Basic information

Entry
Database: PDB / ID: 2hxh
TitleKIF1A head-microtubule complex structure in adp-form
Components
  • Kinesin-like protein KIF1A
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsTRANSPORT PROTEIN / microtubule-based motor
Function / homologyKinesin motor domain / Beta tubulin / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Kinesin-associated / Tubulin / Forkhead-associated (FHA) domain / Kinesin-like protein / Pleckstrin homology domain ...Kinesin motor domain / Beta tubulin / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Kinesin-associated / Tubulin / Forkhead-associated (FHA) domain / Kinesin-like protein / Pleckstrin homology domain / Alpha tubulin / Tubulin/FtsZ, GTPase domain / PH domain / Tubulin/FtsZ, C-terminal / SMAD/FHA domain superfamily / PH-like domain superfamily / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Kinesin motor domain, conserved site / Kinesin-like KIF1-type / Kinesin-like / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin, C-terminal / Kinesin protein 1B / Kinesin motor domain profile. / Forkhead-associated (FHA) domain profile. / PH domain profile. / Kinesin motor domain signature. / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Kinesin-associated / Kinesin motor domain / Kinesin protein / Tubulin C-terminal domain / FHA domain / protein transport along microtubule / interkinetic nuclear migration / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / cytoskeleton-dependent intracellular transport / ATP-dependent microtubule motor activity, plus-end-directed / anterograde axonal transport / kinesin complex / microtubule motor activity / axon cytoplasm / microtubule-based movement / microtubule-based process / presynapse / vesicle-mediated transport / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / postsynapse / synaptic vesicle / mitotic cell cycle / microtubule / microtubule binding / ATPase activity / GTPase activity / neuron projection / axon / GTP binding / dendrite / neuronal cell body / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm / Tubulin alpha-1A chain / Tubulin beta chain / Kinesin-like protein KIF1A
Function and homology information
Specimen sourceMus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 11 Å resolution
AuthorsKikkawa, M. / Hirokawa, N.
CitationJournal: EMBO J. / Year: 2006
Title: High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations.
Authors: Masahide Kikkawa / Nobutaka Hirokawa
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 3, 2006 / Release: Oct 10, 2006
RevisionDateData content typeGroupProviderType
1.0Oct 10, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Kinesin-like protein KIF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6289
Polyers144,3323
Non-polymers2,2966
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 3 types, 3 molecules ABC

#1: Protein/peptide Tubulin alpha chain


Mass: 50121.266 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Genus: Sus / References: UniProt: P02550
#2: Protein/peptide Tubulin beta chain


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Genus: Sus / References: UniProt: P02554
#3: Protein/peptide Kinesin-like protein KIF1A / Axonal transporter of synaptic vesicles


Mass: 44302.855 Da / Num. of mol.: 1 / Fragment: KIF1A head domain / Mutation: P202A / Source: (gene. exp.) Mus musculus (house mouse) / Genus: Mus / Gene: KIF1A / Plasmid name: PET21b / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33173

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: KIF1A head decorated-microtubule complex / Type: COMPLEX
Details: SAMPLE DETAILS: TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED MICROTUBULE WAS PLACED ON THE HOLEY CARBON FILM ON THE EM-GRID AND LEFT FOR 10 S IN THE HUMID CHAMBER. THE MICROTUBULE SOLUTION WAS THEN ABSORBED BY FILTER PAPER, AND A DROP OF THE C351 SOLUTION (0.2 MG/ML) IN THE ASSAY BUFFER (IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M) WAS PUT ON THE GRID. IMMEDIATELY AFTER THE ABSORPTION OF THE DROP, THE GRID WAS PLUNGED INTO LIQUID ETHANE (-185C).
Buffer solutionName: imidazole / Details: imidazole / pH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: Ethan slash

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 2010F / Date: Jan 1, 1999
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 / Calibrated magnification: 40000 / Nominal defocus max: 33000 nm / Nominal defocus min: 11000 nm / Cs: 3.3 mm
Specimen holderTemperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 10 e/Å2 / Details: Scanned with LeafScan45 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1CTFFINDCTF correction
2SITUS COLORESmodel fitting
3RUBY-HELIX3D reconstruction
CTF correctionDetails: each filament
3D reconstructionMethod: Helical / Resolution: 11 Å / Nominal pixel size: 2.5 / Actual pixel size: 2.5 / Magnification calibration: Yes / Symmetry type: HELICAL
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body refinement / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Best cross-correlation
Atomic model building
IDPDB-ID 3D fitting ID
11JFF1
21I5S1
Number of atoms included #LASTProtein: 9237 / Nucleic acid: 0 / Ligand: 151 / Solvent: 0 / Total: 9388

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