+Open data
-Basic information
Entry | Database: PDB / ID: 7ryp | ||||||||||||||||||
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Title | Cryo-EM structure of KIFBP:KIF15 | ||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / kinesin regulation protein | ||||||||||||||||||
Function / homology | Function and homology information plus-end kinesin complex / transport along microtubule / centrosome separation / central nervous system projection neuron axonogenesis / Kinesins / plus-end-directed microtubule motor activity / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex ...plus-end kinesin complex / transport along microtubule / centrosome separation / central nervous system projection neuron axonogenesis / Kinesins / plus-end-directed microtubule motor activity / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / kinesin binding / cytoskeletal motor activity / mitotic spindle assembly / neuron projection maintenance / protein sequestering activity / MHC class II antigen presentation / spindle pole / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / in utero embryonic development / microtubule / cytoskeleton / centrosome / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||
Model details | MODEL GENERATED BY ROSETTA VERSION 2020.08+release.cb1caba | ||||||||||||||||||
Authors | Solon, A.L. / Tan, Z. / Schutt, K.L. / Jepsen, L. / Haynes, S.E. / Nesvizhskii, A.I. / Sept, D. / Stumpff, J. / Ohi, R. / Cianfrocco, M.A. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ryp.cif.gz | 277.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ryp.ent.gz | 225.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ryp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ryp_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ryp_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ryp_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 7ryp_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/7ryp ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7ryp | HTTPS FTP |
-Related structure data
Related structure data | 24744MC 7rsiC 7rsqC 7ryqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 40935.066 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 BL21 (bacteria) / References: UniProt: Q9NS87 |
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#2: 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: cryo-EM structure of KIF15:KIFBP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.7 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101698 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |