[English] 日本語
Yorodumi
- PDB-5hnw: Structural basis of backwards motion in kinesin-14: minus-end dir... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5hnw
TitleStructural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the AMPPNP state
Components
  • Protein claret segregational,KINESIN HEAVY CHAIN ISOFORM 5C
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsTRANSPORT PROTEIN / kinesin / kinesin-14 / microtubule / ATPase
Function / homologyTubulin / Alpha tubulin / Kinesin motor domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin C-terminal domain / Kinesin motor domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily ...Tubulin / Alpha tubulin / Kinesin motor domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin C-terminal domain / Kinesin motor domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain signature. / Beta tubulin / Tubulin/FtsZ, GTPase domain / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Tubulin, C-terminal / Kinesin motor domain, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin-beta mRNA autoregulation signal. / Kinesin motor domain profile. / Tubulin/FtsZ, C-terminal / RHO GTPases activate IQGAPs / Kinesins / Carboxyterminal post-translational modifications of tubulin / 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 / COPI-mediated anterograde transport / RHO GTPases Activate Formins / Intraflagellar transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / MHC class II antigen presentation / Beta tubulin, autoregulation binding site / spindle assembly involved in female meiosis / minus-end directed microtubule sliding / spindle assembly involved in meiosis / regulation of mitotic spindle elongation / distributive segregation / mitotic spindle microtubule / mitotic spindle elongation / meiotic spindle organization / ATP-dependent microtubule motor activity, minus-end-directed / microtubule bundle formation / regulation of mitotic spindle assembly / positive regulation of axon guidance / meiotic spindle / mitotic centrosome separation / kinesin complex / microtubule motor activity / mRNA transport / spindle organization / mitotic spindle assembly / cytoplasmic microtubule / cellular response to interleukin-4 / microtubule-based movement / microtubule-based process / mitotic spindle organization / chromosome segregation / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / microtubule cytoskeleton / spindle / double-stranded RNA binding / mitotic cell cycle / microtubule / microtubule binding / ATPase activity / GTPase activity / centrosome / cell division / GTP binding / ubiquitin protein ligase binding / protein heterodimerization activity / protein homodimerization activity / ATP binding / nucleus / cytosol / cytoplasm / Protein claret segregational / Tubulin alpha-1B chain / Tubulin beta-2B chain
Function and homology information
Specimen sourceDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 6.6 Å resolution
AuthorsShigematsu, H. / Yokoyama, T. / Kikkawa, M. / Shirouzu, M. / Nitta, R.
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility.
Authors: Masahiko Yamagishi / Hideki Shigematsu / Takeshi Yokoyama / Masahide Kikkawa / Mitsuhiro Sugawa / Mari Aoki / Mikako Shirouzu / Junichiro Yajima / Ryo Nitta
Abstract: Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is ...Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is unclear how swinging of the neck helix is driven by ATP hydrolysis utilizing the highly conserved catalytic core among all kinesins. Here, using a motility assay, we show that in addition to the neck helix, the conserved five residues at the C-terminal region in kinesin-14, namely the neck mimic, are necessary to give kinesin-1 an ability to reverse its directionality toward the minus end of microtubules. Our structural analyses further demonstrate that the C-terminal neck mimic, in cooperation with conformational changes in the catalytic core during ATP binding, forms a kinesin-14 bundle with the N-terminal neck helix to swing toward the minus end of microtubules. Thus, the neck mimic plays a crucial role in coupling the chemical ATPase reaction with the mechanical cycle to produce the minus-end-directed motility of kinesin-14.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2016 / Release: Aug 10, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 10, 2016Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelData collection / Database referencescitation / em_image_scans_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jul 25, 2018Structure modelData collection / Database references / Source and taxonomycitation / entity_src_gen_citation.title / _entity_src_gen.gene_src_common_name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8058
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8058
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
K: Protein claret segregational,KINESIN HEAVY CHAIN ISOFORM 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7489
Polyers141,3733
Non-polymers2,3756
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein/peptide , 3 types, 3 molecules ABK

#1: Protein/peptide Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 49976.043 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein/peptide Tubulin beta-2B chain


Mass: 49776.570 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein/peptide Protein claret segregational,KINESIN HEAVY CHAIN ISOFORM 5C / ncd / KIF5C / ncd


Mass: 41620.250 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 325-348, 664-700
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: ncd, CA(ND), CG7831 / Production host: Escherichia coli (E. coli) / References: UniProt: P20480

-
Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Minus-end directed Ncd chimera nKn664COMPLEX1, 2, 30MULTIPLE SOURCES
2Alpha-tubulin 1COMPLEX11NATURAL
3Beta-tubulin 1COMPLEX21NATURAL
4Ncd chimera nKn664COMPLEX31RECOMBINANT
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.719666 deg. / Axial rise/subunit: 8.648646 Å / Axial symmetry: C1
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 229516 / Details: High-resolution noise substitution was performed / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
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

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