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- PDB-7rsi: The cryo-EM map of KIF18A bound to KIFBP -

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Basic information

Entry
Database: PDB / ID: 7rsi
TitleThe cryo-EM map of KIF18A bound to KIFBP
Components
  • KIF-binding protein
  • Kinesin-like protein KIF18A
KeywordsMOTOR PROTEIN / kinesin regualtion protein
Function / homology
Function and homology information


tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / central nervous system projection neuron axonogenesis / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic ...tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / central nervous system projection neuron axonogenesis / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / mitotic metaphase chromosome alignment / mitochondrial transport / microtubule-based movement / seminiferous tubule development / mitotic sister chromatid segregation / kinesin binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of microtubule cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / ruffle / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / neuron projection maintenance / cellular response to estradiol stimulus / caveola / RHO GTPases Activate Formins / microtubule cytoskeleton organization / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / protein transport / actin binding / microtubule binding / in utero embryonic development / cytoskeleton / centrosome / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
KIF-1 binding protein / KIF-1 binding protein C terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...KIF-1 binding protein / KIF-1 binding protein C terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / 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 / Kinesin-like protein KIF18A / KIF-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsTan, Z. / Solon, A.L. / Schutt, K.L. / Jepsen, L. / Haynes, S.E. / Nesvizhskii, A.I. / Sept, D. / Stumpff, J. / Ohi, R. / Cianfrocco, M.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086610 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136822 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121491 United States
CitationJournal: Sci Adv / Year: 2021
Title: Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding.
Authors: April L Solon / Zhenyu Tan / Katherine L Schutt / Lauren Jepsen / Sarah E Haynes / Alexey I Nesvizhskii / David Sept / Jason Stumpff / Ryoma Ohi / Michael A Cianfrocco /
Abstract: Kinesins are regulated in space and time to ensure activation only in the presence of cargo. Kinesin-binding protein (KIFBP), which is mutated in Goldberg-Shprintzen syndrome, binds to and inhibits ...Kinesins are regulated in space and time to ensure activation only in the presence of cargo. Kinesin-binding protein (KIFBP), which is mutated in Goldberg-Shprintzen syndrome, binds to and inhibits the catalytic motor heads of 8 of 45 kinesin superfamily members, but the mechanism remains poorly defined. Here, we used cryo–electron microscopy and cross-linking mass spectrometry to determine high-resolution structures of KIFBP alone and in complex with two mitotic kinesins, revealing structural remodeling of kinesin by KIFBP. We find that KIFBP remodels kinesin motors and blocks microtubule binding (i) via allosteric changes to kinesin and (ii) by sterically blocking access to the microtubule. We identified two regions of KIFBP necessary for kinesin binding and cellular regulation during mitosis. Together, this work further elucidates the molecular mechanism of KIFBP-mediated kinesin inhibition and supports a model in which structural rearrangement of kinesin motor domains by KIFBP abrogates motor protein activity.
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
B: KIF-binding protein
C: Kinesin-like protein KIF18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9254
Polymers111,4742
Non-polymers4522
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2760 Å2
ΔGint-23 kcal/mol
Surface area36670 Å2

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q96EK5
#2: Protein Kinesin-like protein KIF18A / Marrow stromal KIF18A / MS-KIF18A


Mass: 39560.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF18A, OK/SW-cl.108
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8NI77
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: KIFBP:KIF18A complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54801 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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