[English] 日本語
Yorodumi
- PDB-5nd7: Microtubule-bound MKLP2 motor domain in the presence of AMPPNP -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5nd7
TitleMicrotubule-bound MKLP2 motor domain in the presence of AMPPNP
DescriptorKinesin-like protein KIF20A
Tubulin alpha chain
Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin Mitosis Microtubules / Motor protein
Specimen sourceMus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Bos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (7.9 Å resolution / Filament / Single particle)
AuthorsAtherton, J. / Yu, I.-M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. / Houdusse, A. / Moores, C.A.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Release: Oct 4, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
C: Kinesin-like protein KIF20A
A: Tubulin alpha chain
B: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,4119
Polyers156,0363
Non-polymers2,3756
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)9950
ΔGint (kcal/M)-59
Surface area (Å2)44070
MethodPISA
Conformers5 models

-
Components

-
Polypeptide(L) , 3 types, 3 molecules CAB

#1: Polypeptide(L)Kinesin-like protein KIF20A / Kinesin-like protein 174 / Rab6-interacting kinesin-like protein / Rabkinesin-6


Mass: 56021.332 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus / References: UniProt: P97329
#2: Polypeptide(L)Tubulin alpha chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#3: Polypeptide(L)Tubulin beta-2B chain


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q6B856

-
Non-polymers , 5 types, 6 molecules

#4: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg
#5: ChemicalChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP (energy-carrying molecule analogue) *YM


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3
#6: ChemicalChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP *YM


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3
#7: ChemicalChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP *YM


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2
#8: ChemicalChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component

Details: Microtubule bound to taxol / Type: COMPLEX

IDNameEntity IDParent IDSource
1Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of AMPPNP1, 2, 30MULTIPLE SOURCES
2Kinesin-like protein KIF20A11RECOMBINANT
3Tubulin alpha and beta chains2, 31NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1110090Mus musculus
229913Bos taurus
Source (recombinant)Organism: Escherichia coli
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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10858
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)
Symmetry type: POINT

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more