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- PDB-9ko8: Crystal structure of Hook3(553-624) bound to KIF1C(714-809) -

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Basic information

Entry
Database: PDB / ID: 9ko8
TitleCrystal structure of Hook3(553-624) bound to KIF1C(714-809)
Components
  • Kinesin-like protein KIF1C
  • Protein Hook homolog 3
KeywordsTRANSPORT PROTEIN / Hook3 / KIF1C
Function / homology
Function and homology information


FHF complex / interkinetic nuclear migration / Golgi localization / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / anterograde neuronal dense core vesicle transport / dynein light chain binding / retrograde neuronal dense core vesicle transport / cytoskeleton-dependent intracellular transport / neuronal stem cell population maintenance ...FHF complex / interkinetic nuclear migration / Golgi localization / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / anterograde neuronal dense core vesicle transport / dynein light chain binding / retrograde neuronal dense core vesicle transport / cytoskeleton-dependent intracellular transport / neuronal stem cell population maintenance / endosome organization / early endosome to late endosome transport / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / protein localization to centrosome / dynein light intermediate chain binding / dynein intermediate chain binding / lysosome organization / COPI-dependent Golgi-to-ER retrograde traffic / endosome to lysosome transport / pericentriolar material / cytoskeletal motor activity / dynactin binding / vesicle-mediated transport / cytoplasmic microtubule organization / axon cytoplasm / negative regulation of neurogenesis / centriolar satellite / protein transport / microtubule binding / microtubule / axon / centrosome / dendrite / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Hook, C-terminal / HOOK protein coiled-coil region / HOOK, N-terminal / HOOK domain / Kinesin-associated / Kinesin-associated / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site ...Hook, C-terminal / HOOK protein coiled-coil region / HOOK, N-terminal / HOOK domain / Kinesin-associated / Kinesin-associated / 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 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF1C / Protein Hook homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKu, B. / Lee, H.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)KGM9952421 Korea, Republic Of
Other governmentCRC22021-700 Korea, Republic Of
CitationJournal: Embo Rep. / Year: 2025
Title: Molecular basis for assembly and activation of the Hook3 - KIF1C complex-dependent transport machinery.
Authors: Lee, H.S. / Yu, D. / Baek, K.E. / Shin, H.C. / Kim, S.J. / Do Heo, W. / Ku, B.
History
DepositionNov 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF1C
B: Kinesin-like protein KIF1C
C: Protein Hook homolog 3
D: Protein Hook homolog 3


Theoretical massNumber of molelcules
Total (without water)40,8894
Polymers40,8894
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.562, 166.946, 39.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Kinesin-like protein KIF1C


Mass: 11343.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1C, KIAA0706 / Production host: Escherichia coli (E. coli) / References: UniProt: O43896
#2: Protein Protein Hook homolog 3 / h-hook3 / hHK3


Mass: 9101.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOOK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VS8
#3: Water ChemComp-HOH / water


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

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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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate/citric acid (pH 5.5), 20% (w/v) polyethylene glycol 4000, and 20% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9356 / % possible obs: 93.6 % / Redundancy: 4.6 % / Rsym value: 0.117 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 371 / Rsym value: 0.263

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9KNS

9kns


Resolution: 3→45.671 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 29.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2914 723 9.99 %
Rwork0.2412 --
obs0.2465 7239 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→45.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 27 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012167
X-RAY DIFFRACTIONf_angle_d1.2012892
X-RAY DIFFRACTIONf_dihedral_angle_d20.2481374
X-RAY DIFFRACTIONf_chiral_restr0.056315
X-RAY DIFFRACTIONf_plane_restr0.007372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.23170.32331320.24911203X-RAY DIFFRACTION90
3.2317-3.55680.31931430.24571293X-RAY DIFFRACTION96
3.5568-4.07120.28771440.2181286X-RAY DIFFRACTION96
4.0712-5.12810.29371470.2251312X-RAY DIFFRACTION95
5.1281-45.6710.26711570.26481422X-RAY DIFFRACTION96

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