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- EMDB-24672: The cryo-EM map of KIF18A bound to KIFBP -

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Basic information

Entry
Database: EMDB / ID: EMD-24672
TitleThe cryo-EM map of KIF18A bound to KIFBP
Map data
Sample
  • Complex: KIFBP:KIF18A complex
    • Protein or peptide: KIF-binding protein
    • Protein or peptide: Kinesin-like protein KIF18A
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordskinesin regualtion protein / MOTOR PROTEIN
Function / homology
Function and homology information


tubulin-dependent ATPase activity / mitotic spindle astral microtubule / transport along 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 ...tubulin-dependent ATPase activity / mitotic spindle astral microtubule / transport along 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 / microtubule depolymerization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / mitotic metaphase chromosome alignment / 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 / neuron projection maintenance / protein sequestering activity / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to estradiol stimulus / RHO GTPases Activate Formins / caveola / kinetochore / microtubule cytoskeleton organization / 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 profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 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 profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF18A / KIF-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsTan Z / Solon AL
Funding support United States, 4 items
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, 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: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rsi
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rsi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24672.png

Downloads & links

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Map

FileDownload / File: emd_24672.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.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.1419493 - 0.5281409
Average (Standard dev.)0.000058942376 (±0.013282277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z273.000273.000273.000
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-0.1420.5280.000

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Supplemental data

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Mask #1

Fileemd_24672_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_24672_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24672_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24672_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : KIFBP:KIF18A complex

EntireName: KIFBP:KIF18A complex
Components
  • Complex: KIFBP:KIF18A complex
    • Protein or peptide: KIF-binding protein
    • Protein or peptide: Kinesin-like protein KIF18A
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: KIFBP:KIF18A complex

SupramoleculeName: KIFBP:KIF18A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: KIF-binding protein

MacromoleculeName: KIF-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.913945 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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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Macromolecule #2: Kinesin-like protein KIF18A

MacromoleculeName: Kinesin-like protein KIF18A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.560008 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSVTEEDLCH HMKVVVRVRP ENTKEKAAGF HKVVHVVDKH ILVFDPKQEE VSFFHGKKTT NQNVIKKQNK DLKFVFDAVF DETSTQSEV FEHTTKPILR SFLNGYNCTV LAYGATGAGK THTMLGSADE PGVMYLTMLH LYKCMDEIKE EKICSTAVSY L EVYNEQIR ...String:
MSVTEEDLCH HMKVVVRVRP ENTKEKAAGF HKVVHVVDKH ILVFDPKQEE VSFFHGKKTT NQNVIKKQNK DLKFVFDAVF DETSTQSEV FEHTTKPILR SFLNGYNCTV LAYGATGAGK THTMLGSADE PGVMYLTMLH LYKCMDEIKE EKICSTAVSY L EVYNEQIR DLLVNSGPLA VREDTQKGVV VHGLTLHQPK SSEEILHLLD NGNKNRTQHP TDMNATSSRS HAVFQIYLRQ QD KTASINQ NVRIAKMSLI DLAGSERAST SGAKGTRFVE GTNINRSLLA LGNVINALAD SKRKNQHIPY RNSKLTRLLK DSL GGNCQT IMIAAVSPSS VFYDDTYNTL KYANRAK

UniProtKB: Kinesin-like protein KIF18A

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration0.5 mg/mL
BufferpH: 7.7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryosparc ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54801
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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