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- PDB-6zpi: Microtubule complexed with Kif15 motor domain. Symmetrised asymme... -

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Basic information

Entry
Database: PDB / ID: 6zpi
TitleMicrotubule complexed with Kif15 motor domain. Symmetrised asymmetric unit
Components
  • Kinesin-like protein KIF15
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / Kinesin / microtubules / kinesin binding protein / KBP
Function / homology
Function and homology information


plus-end kinesin complex / centrosome separation / plus-end-directed microtubule motor activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase ...plus-end kinesin complex / centrosome separation / plus-end-directed microtubule motor activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Kinesins / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / kinesin complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule motor activity / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly / MHC class II antigen presentation / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle pole / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF15
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
C: Kinesin-like protein KIF15
A: Tubulin alpha-1B chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5119
Polymers138,1353
Non-polymers2,3756
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10240 Å2
ΔGint-58 kcal/mol
Surface area44190 Å2
MethodPISA

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Components

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Protein , 3 types, 3 molecules CAB

#1: Protein Kinesin-like protein KIF15 / Kinesin-like protein 2 / hKLP2 / Kinesin-like protein 7 / Serologically defined breast cancer antigen NY-BR-62


Mass: 41157.133 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
#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48679.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#3: Protein Tubulin beta chain / Beta-tubulin


Mass: 48299.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Kif15 motor domain (AMPPNP bound) complexed with microtubule. Symmetrised asymmetric unit.COMPLEX#1-#30MULTIPLE SOURCES
2Kif15 motor domainCOMPLEX#11RECOMBINANT
3MicrotubuleCOMPLEX#2-#31NATURAL
Molecular weightValue: 0.072 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Sus scrofa (pig)9823
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
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

EM software
IDNameCategoryDetails
11RELIONfinal Euler assignment
13RELION3D reconstructionMiRP protocol
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12674 / Symmetry type: POINT

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