[English] 日本語
Yorodumi
- PDB-2wbe: Kinesin-5-Tubulin Complex with AMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wbe
TitleKinesin-5-Tubulin Complex with AMPPNP
Components
  • BIPOLAR KINESIN KRP-130
  • TUBULIN ALPHA-1D CHAIN
  • TUBULIN BETA-2B CHAIN
KeywordsSTRUCTURAL PROTEIN / EG5 / KLP61F / KINESIN / TUBULIN / MITOSIS / KINESIN-5 / GTP-BINDING / MOTOR PROTEIN / CELL DIVISION / CELL CYCLE / MICROTUBULE / ATP-BINDING / HOMOLOGY MODEL / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport / microtubule bundle formation / plus-end-directed microtubule motor activity / mitotic centrosome separation / positive regulation of axon guidance / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / microtubule-based process / mitotic spindle organization / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha-1A chain / Tubulin beta chain / Kinesin-like protein Klp61F / Tubulin alpha-1D chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
BOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsBodey, A.J. / Kikkawa, M. / Moores, C.A.
CitationJournal: J Mol Biol / Year: 2009
Title: 9-Angström structure of a microtubule-bound mitotic motor.
Authors: Andrew J Bodey / Masahide Kikkawa / Carolyn A Moores /
Abstract: Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the ...Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the nature of the K5-MT interaction and the regulatory mechanisms that control it remain unclear. Using cryo-electron microscopy and image processing, we calculated the structure of a K5 motor bound to MTs at 9 A resolution, providing insight into this important interaction. Our reconstruction reveals the K5 motor domain in an ATP-like conformation in which MT binding induces the conserved nucleotide-sensing switch I and II loops to form a compact subdomain around the bound nucleotide. Our reconstruction also reveals a novel conformation for the K5-specific drug-binding loop 5, suggesting a possible role for it in switching K5s between force generation and diffusional modes of MT binding. Our data thus shed light on regulation of the interaction between spindle components important for chromosome segregation.
History
DepositionFeb 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 27, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Oct 3, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id / _em_software.name
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1604
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1604
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1604
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUBULIN ALPHA-1D CHAIN
B: TUBULIN BETA-2B CHAIN
C: BIPOLAR KINESIN KRP-130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3029
Polymers141,9273
Non-polymers2,3756
Water0
1
A: TUBULIN ALPHA-1D CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6553
Polymers50,1071
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TUBULIN BETA-2B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2053
Polymers49,9081
Non-polymers1,2972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BIPOLAR KINESIN KRP-130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4423
Polymers41,9121
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein TUBULIN ALPHA-1D CHAIN / ALPHA-BETA-TUBULIN / TUBA1D


Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P02550, UniProt: Q2HJ86*PLUS
#2: Protein TUBULIN BETA-2B CHAIN / ALPHA-BETA-TUBULIN / TUBB2B


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P02554, UniProt: Q6B856*PLUS
#3: Protein BIPOLAR KINESIN KRP-130 / KLP61F / KINESIN-LIKE PROTEIN KLP61F / KLP2


Mass: 41911.566 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN WITH NECK LINKER, RESIDUES 1-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET-15B-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46863

-
Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-TA1 / TAXOL / Paclitaxel


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Details

Nonpolymer detailsPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): NON-HYDROLYSABLE ATP ANALOGUE

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: MICROTUBULE-KLP61F COMPLEX WITH AMPPNP / Type: COMPLEX
Buffer solutionName: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL
pH: 6.8
Details: 80MM PIPES, 150MM NACL, 7MM MGCL2, 1MM EGTA, 1MM BETA-MERCAPTOETHANOL
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3940 nm / Nominal defocus min: 1080 nm / Cs: 2 mm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 24

-
Processing

EM softwareName: Ruby-Helix / Category: 3D reconstruction
CTF correctionDetails: PHASE FLIPPING, WIENER
3D reconstructionMethod: HELICAL PROCESSING / Resolution: 9.4 Å / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å
Details: THE KLP61F HOMOLOGY MODEL WAS GENERATED WITH MODELLER 9V1 AND THE FOLLOWING TEMPLATES - 1MKJ.PDB, 1T5C.PDB AND 2KIN.PDB
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER
Details: REFINEMENT PROTOCOL--HOMOLOGY (KLP61F), ELECTRON CRYSTALLOGRAPHY (TUBULIN)
Atomic model building
IDPDB-ID 3D fitting-ID
11MKJ

1mkj

1
21T5C

1t5c

1
32KIN

2kin

1
RefinementHighest resolution: 9.4 Å
Refinement stepCycle: LAST / Highest resolution: 9.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9230 0 155 0 9385

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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