[English] 日本語
Yorodumi
- EMDB-3780: Molecular basis of human kinesin-8 function and inhibition -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3780
TitleMolecular basis of human kinesin-8 function and inhibition
Map dataAsymmetric unit extracted from the full MT-bound Kif18A motor domain AMPPNP-bound reconstruction
Sample13-Protofilament microtuble-bound human Kinesin-8 motor domain neck-linker with AMPPNP:
Kinesin-8 motor domain neck-linker / Tubulin, alpha / Tubulin, beta / Kinesin-like protein KIF18A / Tubulin alpha chain / Tubulin beta chain / (ligand) x 6
Function / homologyTubulin, C-terminal / Kinesin motor domain superfamily / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site ...Tubulin, C-terminal / Kinesin motor domain superfamily / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Kinesin motor domain, conserved site / Hedgehog 'off' state / P-loop containing nucleoside triphosphate hydrolase / Kinesin-like protein / Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Recycling pathway of L1 / MHC class II antigen presentation / Recruitment of mitotic centrosome proteins and complexes / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Tubulin/FtsZ family, GTPase domain / Kinesin motor domain profile. / Kinesin motor domain signature. / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Tubulin C-terminal domain / Kinesin motor domain / Cilium Assembly / Recruitment of NuMA to mitotic centrosomes / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / RHO GTPases Activate Formins / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / MHC class II antigen presentation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Anchoring of the basal body to the plasma membrane / Intraflagellar transport / RHO GTPases activate IQGAPs / Kinesins / COPI-mediated anterograde transport / RHO GTPases Activate Formins / Hedgehog 'on' state / tubulin-dependent ATPase activity / kinetochore microtubule / mitotic spindle midzone / male meiotic nuclear division / microtubule plus-end binding / seminiferous tubule development / microtubule depolymerization / ATP-dependent microtubule motor activity, plus-end-directed / mitotic metaphase plate congression / kinesin complex / retrograde vesicle-mediated transport, Golgi to ER / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule / cellular response to interleukin-4 / recycling endosome / microtubule-based process / microtubule cytoskeleton organization / antigen processing and presentation of exogenous peptide antigen via MHC class II / kinetochore / microtubule-based movement / cytoplasmic ribonucleoprotein granule / structural constituent of cytoskeleton / ruffle / microtubule cytoskeleton / cellular response to estradiol stimulus / microtubule organizing center / caveola / double-stranded RNA binding / protein transport / actin binding / microtubule / microtubule binding / GTPase activity / myelin sheath / GTP binding / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm / Tubulin alpha chain / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF18A
Function and homology information
SourceHomo sapiens (human) / Bos taurus (cattle) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / 5.2 Å resolution
AuthorsLocke J / Joseph AP
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of human kinesin-8 function and inhibition.
Authors: Julia Locke / Agnel Praveen Joseph / Alejandro Peña / Martin M Möckel / Thomas U Mayer / Maya Topf / Carolyn A Moores
Abstract: Kinesin motors play diverse roles in mitosis and are targets for antimitotic drugs. The clinical significance of these motors emphasizes the importance of understanding the molecular basis of their ...Kinesin motors play diverse roles in mitosis and are targets for antimitotic drugs. The clinical significance of these motors emphasizes the importance of understanding the molecular basis of their function. Equally important, investigations into the modes of inhibition of these motors provide crucial information about their molecular mechanisms. Kif18A regulates spindle microtubules through its dual functionality, with microtubule-based stepping and regulation of microtubule dynamics. We investigated the mechanism of Kif18A and its inhibition by the small molecule BTB-1. The Kif18A motor domain drives ATP-dependent plus-end microtubule gliding, and undergoes conformational changes consistent with canonical mechanisms of plus-end-directed motility. The Kif18A motor domain also depolymerizes microtubule plus and minus ends. BTB-1 inhibits both of these microtubule-based Kif18A activities. A reconstruction of BTB-1-bound, microtubule-bound Kif18A, in combination with computational modeling, identified an allosteric BTB-1-binding site near loop5, where it blocks the ATP-dependent conformational changes that we characterized. Strikingly, BTB-1 binding is close to that of well-characterized Kif11 inhibitors that block tight microtubule binding, whereas BTB-1 traps Kif18A on the microtubule. Our work highlights a general mechanism of kinesin inhibition in which small-molecule binding near loop5 prevents a range of conformational changes, blocking motor function.
Validation ReportPDB-ID: 5ocu

SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Oct 25, 2017 / Last update: Nov 15, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ocu
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3780.map.gz (map file in CCP4 format, 1953 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
69 pix
1.39 Å/pix.
= 95.91 Å
54 pix
1.39 Å/pix.
= 75.06 Å
131 pix
1.39 Å/pix.
= 182.09 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.031056289 - 0.19615224
Average (Standard dev.)0.019010613 (0.035334263)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions5413169
Origin20663146
Limit259193214
Spacing1315469
CellA: 182.09 Å / B: 75.06 Å / C: 95.909996 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z1315469
origin x/y/z0.0000.0000.000
length x/y/z182.09075.06095.910
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS63206146
NC/NR/NS1315469
D min/max/mean-0.0310.1960.019

-
Supplemental data

-
Sample components

+
Entire 13-Protofilament microtuble-bound human Kinesin-8 motor domain ne...

EntireName: 13-Protofilament microtuble-bound human Kinesin-8 motor domain neck-linker with AMPPNP
Number of components: 13

+
Component #1: protein, 13-Protofilament microtuble-bound human Kinesin-8 motor ...

ProteinName: 13-Protofilament microtuble-bound human Kinesin-8 motor domain neck-linker with AMPPNP
Recombinant expression: No

+
Component #2: protein, Kinesin-8 motor domain neck-linker

ProteinName: Kinesin-8 motor domain neck-linker / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #3: protein, Tubulin, alpha

ProteinName: Tubulin, alpha / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

+
Component #4: protein, Tubulin, beta

ProteinName: Tubulin, beta / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

+
Component #5: protein, Kinesin-like protein KIF18A

ProteinName: Kinesin-like protein KIF18A / Recombinant expression: No
MassTheoretical: 42.213938 kDa
Source (engineered)Expression System: Homo sapiens (human)

+
Component #6: protein, Tubulin alpha chain

ProteinName: Tubulin alpha chain / Recombinant expression: No
MassTheoretical: 50.107238 kDa
SourceSpecies: Bos taurus (cattle)

+
Component #7: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Sus scrofa (pig)

+
Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #9: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

+
Component #10: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #11: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #12: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

+
Component #13: ligand, TAXOL

LigandName: TAXOLPaclitaxel / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.853906 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 81 Å
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Details: FEI Polara
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - nm / Energy filter: GIF Quantum
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more