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- EMDB-24677: Cryo-EM structure of KIFBP core -

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Basic information

Entry
Database: EMDB / ID: EMD-24677
TitleCryo-EM structure of KIFBP core
Map data
Sample
  • Complex: high-resolution structure of KIFBP(core)
    • Protein or peptide: KIF-binding protein
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / mitochondrial transport / kinesin binding / neuron projection maintenance / microtubule cytoskeleton organization / in utero embryonic development / cytoskeleton / mitochondrion
Similarity search - Function
KIF-1 binding protein / KIF-1 binding protein C terminal / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSolon AL / Tan Z / Schutt KL / Jepsen L / Haynes SE / Nesvizhskii AI / Sept D / Stumpff J / Ohi R / Cianfrocco MA
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 11, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rsq
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rsq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24677.png

Downloads & links

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Map

FileDownload / File: emd_24677.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.05381098 - 0.074899435
Average (Standard dev.)1.9904217e-06 (±0.0016051247)
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-0.0540.0750.000

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Supplemental data

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Mask #1

Fileemd_24677_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_24677_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24677_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24677_half_map_2.map
Projections & Slices
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Sample components

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Entire : high-resolution structure of KIFBP(core)

EntireName: high-resolution structure of KIFBP(core)
Components
  • Complex: high-resolution structure of KIFBP(core)
    • Protein or peptide: KIF-binding protein

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Supramolecule #1: high-resolution structure of KIFBP(core)

SupramoleculeName: high-resolution structure of KIFBP(core) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 (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

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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

Concentration4 mg/mL
BufferpH: 7.7
GridModel: UltrAuFoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

Particle selectionNumber selected: 128190
CTF correctionSoftware - Name: cryoSPARC
Startup modelType of model: OTHER / Details: cryosparc ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128190

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7rsq:
Cryo-EM structure of KIFBP core

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