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- EMDB-11338: Kinesin binding protein (KBP) -

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Basic information

Entry
Database: EMDB / ID: EMD-11338
TitleKinesin binding protein (KBP)
Map dataKinesin binding protein (KBP) sharpened/filtered cryo-EM density.
Sample
  • Complex: Kinesin binding protein cryo-EM density
    • Protein or peptide: KIF-binding protein
KeywordsKinesin / microtubules / kinesin binding protein / KBP / MOTOR PROTEIN
Function / homology
Function and homology information


transport along microtubule / central nervous system projection neuron axonogenesis / mitochondrion transport along microtubule / kinesin binding / neuron projection maintenance / protein sequestering activity / 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: 4.6 Å
AuthorsAtherton J / Hummel JJA
Funding support United Kingdom, Switzerland, United States, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R000352/1 United Kingdom
Worldwide Cancer Research16-0037 United Kingdom
Swiss National Science Foundation31003A_166608 Switzerland
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130556 United States
CitationJournal: Elife / Year: 2020
Title: The mechanism of kinesin inhibition by kinesin-binding protein.
Authors: Joseph Atherton / Jessica Ja Hummel / Natacha Olieric / Julia Locke / Alejandro Peña / Steven S Rosenfeld / Michel O Steinmetz / Casper C Hoogenraad / Carolyn A Moores /
Abstract: Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of ...Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain's tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity.
History
DepositionJul 8, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zpg
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11338.png

Downloads & links

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Map

FileDownload / File: emd_11338.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKinesin binding protein (KBP) sharpened/filtered cryo-EM density.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 180 pix.
= 187.74 Å		1.04 Å/pix.
x 180 pix.
= 187.74 Å		1.04 Å/pix.
x 180 pix.
= 187.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.043 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0235 / Movie #1: 0.0235
Minimum - Maximum-0.06600354 - 0.12910874
Average (Standard dev.)0.00013371636 (±0.0033123507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 187.73999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0431.0431.043
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z187.740187.740187.740
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0660.1290.000

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Supplemental data

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Sample components

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Entire : Kinesin binding protein cryo-EM density

EntireName: Kinesin binding protein cryo-EM density
Components
  • Complex: Kinesin binding protein cryo-EM density
    • Protein or peptide: KIF-binding protein

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Supramolecule #1: Kinesin binding protein cryo-EM density

SupramoleculeName: Kinesin binding protein cryo-EM density / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72 KDa

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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 (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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Details: Movies were collected with a volta phase plate.Movies were dose weighted.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: De novo generated model in cryoSPARC2.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258049
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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