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- PDB-6zph: Kinesin binding protein complexed with Kif15 motor domain -

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Basic information

Entry
Database: PDB / ID: 6zph
TitleKinesin binding protein complexed with Kif15 motor domain
Components
  • KIF-binding protein
  • Kinesin-like protein KIF15
KeywordsMOTOR PROTEIN / Kinesin / microtubules / kinesin binding protein / KBP
Function / homology
Function and homology information


plus-end kinesin complex / centrosome separation / transport along microtubule / central nervous system projection neuron axonogenesis / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule motor activity / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic ...plus-end kinesin complex / centrosome separation / transport along microtubule / central nervous system projection neuron axonogenesis / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule motor activity / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / cytoskeletal motor activity / kinesin binding / mitotic spindle assembly / neuron projection maintenance / MHC class II antigen presentation / protein sequestering activity / microtubule cytoskeleton organization / spindle pole / mitotic cell cycle / microtubule binding / in utero embryonic development / microtubule / cytoskeleton / centrosome / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / KIF-1 binding protein / KIF-1 binding protein C terminal / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / KIF-1 binding protein / KIF-1 binding protein C terminal / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / KIF-binding protein / Kinesin-like protein KIF15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsAtherton, J. / Hummel, J.J.A. / Olieric, N. / Locke, J. / Pena, A. / Rosenfeld, S.S. / Steinmetz, M.O. / Hoogenraad, C.C. / Moores, C.A.
Funding support United Kingdom, Switzerland, United States, 6items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R000352/1 United Kingdom
Worldwide Cancer Research16-0037 United Kingdom
Swiss National Science Foundation31003A_166608 Switzerland
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130556 United States
CitationJournal: Elife / Year: 2020
Title: The mechanism of kinesin inhibition by kinesin-binding protein.
Authors: Joseph Atherton / Jessica Ja Hummel / Natacha Olieric / Julia Locke / Alejandro Peña / Steven S Rosenfeld / Michel O Steinmetz / Casper C Hoogenraad / Carolyn A Moores /
Abstract: Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of ...Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain's tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.0Dec 30, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 30, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 30, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 30, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 30, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: KIF-binding protein
B: Kinesin-like protein KIF15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3514
Polymers113,9002
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4170 Å2
ΔGint-21 kcal/mol
Surface area45880 Å2
MethodPISA

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Components

#1: Protein KIF-binding protein / KIF1-binding protein / Kinesin family binding protein


Mass: 71913.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIFBP, KBP, KIAA1279, KIF1BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EK5
#2: Protein Kinesin-like protein KIF15 / Kinesin-like protein 2 / hKLP2 / Kinesin-like protein 7 / Serologically defined breast cancer antigen NY-BR-62


Mass: 41986.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF15, KLP2, KNSL7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NS87
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Kinesin binding protein complexed with Kif15 motor domain cryo-EM density
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.072 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Details: Movies were dose weighted.

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
8PHENIXmodel refinement
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7513 / Symmetry type: POINT

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