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- EMDB-24744: Cryo-EM structure of KIFBP:KIF15 -

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Basic information

Entry
Database: EMDB / ID: EMD-24744
TitleCryo-EM structure of KIFBP:KIF15
Map data
Sample
  • Complex: cryo-EM structure of KIF15:KIFBP
    • Protein or peptide: Kinesin-like protein KIF15
    • Protein or peptide: KIF-binding protein
Keywordskinesin regulation protein / MOTOR 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 / cytoskeletal motor activity / kinesin binding / mitotic spindle assembly / neuron projection maintenance / protein sequestering activity / MHC class II antigen presentation / microtubule cytoskeleton organization / spindle pole / mitotic cell cycle / microtubule binding / in utero embryonic development / microtubule / cytoskeleton / centrosome / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / 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
KIF-binding protein / Kinesin-like protein KIF15
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsSolon AL / Tan Z
Funding support United States, 5 items
OrganizationGrant numberCountry
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
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)GM111725 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 25, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ryp
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ryp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24744.png

Downloads & links

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Map

FileDownload / File: emd_24744.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 300 pix.
= 294. Å		0.98 Å/pix.
x 300 pix.
= 294. Å		0.98 Å/pix.
x 300 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-0.24530536 - 0.61500365
Average (Standard dev.)0.00023199662 (±0.01537278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2450.6150.000

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Supplemental data

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Mask #1

Fileemd_24744_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_24744_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24744_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_24744_half_map_2.map
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Sample components

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Entire : cryo-EM structure of KIF15:KIFBP

EntireName: cryo-EM structure of KIF15:KIFBP
Components
  • Complex: cryo-EM structure of KIF15:KIFBP
    • Protein or peptide: Kinesin-like protein KIF15
    • Protein or peptide: KIF-binding protein

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Supramolecule #1: cryo-EM structure of KIF15:KIFBP

SupramoleculeName: cryo-EM structure of KIF15:KIFBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Kinesin-like protein KIF15

MacromoleculeName: Kinesin-like protein KIF15 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.935066 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAPGCKTELR SVTNGQSNQP SNEGDAIKVF VRIRPPAERS GSADGEQNLC LSVLSSTSLR LHSNPEPKTF TFDHVADVDT TQESVFATV AKSIVESCMS GYNGTIFAYG QTGSGKTFTM MGPSESDNFS HNLRGVIPRS FEYLFSLIDR EKEKAGAGKS F LCKCSFIE ...String:
MAPGCKTELR SVTNGQSNQP SNEGDAIKVF VRIRPPAERS GSADGEQNLC LSVLSSTSLR LHSNPEPKTF TFDHVADVDT TQESVFATV AKSIVESCMS GYNGTIFAYG QTGSGKTFTM MGPSESDNFS HNLRGVIPRS FEYLFSLIDR EKEKAGAGKS F LCKCSFIE IYNEQIYDLL DSASAGLYLR EHIKKGVFVV GAVEQVVTSA AEAYQVLSGG WRNRRVASTS MNRESSRSHA VF TITIESM EKSNEIVNIR TSLLNLVDLA GSERQKDTHA EGMRLKEAGN INRSLSCLGQ VITALVDVGN GKQRHVCYRD SKL TFLLRD SLGGNAKTAI IANVHPGSRC FGETLSTLNF AQRAKLIKNK AVVNEDTQG

UniProtKB: Kinesin-like protein KIF15

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Macromolecule #2: KIF-binding protein

MacromoleculeName: KIF-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.913945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANVPWAEVC EKFQAALALS RVELHKNPEK EPYKSKYSAR ALLEEVKALL GPAPEDEDER PEAEDGPGAG DHALGLPAEV VEPEGPVAQ RAVRLAVIEF HLGVNHIDTE ELSAGEEHLV KCLRLLRRYR LSHDCISLCI QAQNNLGILW SEREEIETAQ A YLESSEAL ...String:
MANVPWAEVC EKFQAALALS RVELHKNPEK EPYKSKYSAR ALLEEVKALL GPAPEDEDER PEAEDGPGAG DHALGLPAEV VEPEGPVAQ RAVRLAVIEF HLGVNHIDTE ELSAGEEHLV KCLRLLRRYR LSHDCISLCI QAQNNLGILW SEREEIETAQ A YLESSEAL YNQYMKEVGS PPLDPTERFL PEEEKLTEQE RSKRFEKVYT HNLYYLAQVY QHLEMFEKAA HYCHSTLKRQ LE HNAYHPI EWAINAATLS QFYINKLCFM EARHCLSAAN VIFGQTGKIS ATEDTPEAEG EVPELYHQRK GEIARCWIKY CLT LMQNAQ LSMQDNIGEL DLDKQSELRA LRKKELDEEE SIRKKAVQFG TGELCDAISA VEEKVSYLRP LDFEEARELF LLGQ HYVFE AKEFFQIDGY VTDHIEVVQD HSALFKVLAF FETDMERRCK MHKRRIAMLE PLTVDLNPQY YLLVNRQIQF EIAHA YYDM MDLKVAIADR LRDPDSHIVK KINNLNKSAL KYYQLFLDSL RDPNKVFPEH IGEDVLRPAM LAKFRVARLY GKIITA DPK KELENLATSL EHYKFIVDYC EKHPEAAQEI EVELELSKEM VSLLPTKMER FRTKMALT

UniProtKB: KIF-binding protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: cryosparc ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101698
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ryp:
Cryo-EM structure of KIFBP:KIF15

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