[English] 日本語
Yorodumi
- PDB-2p4n: Human Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked i... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2p4n
TitleHuman Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked into the 9-Angstrom Cryo-EM Map of Nucleotide-Free Kinesin Complexed to the Microtubule
Components
  • Kinesin heavy chain
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsTRANSPORT PROTEIN / Motor protein / ATPase
Function / homologyTubulin / Kinesin motor domain, conserved site / Recycling pathway of L1 / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Resolution of Sister Chromatid Cohesion / Kinesin motor domain / Alpha tubulin / Beta tubulin ...Tubulin / Kinesin motor domain, conserved site / Recycling pathway of L1 / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Resolution of Sister Chromatid Cohesion / 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 / Tubulin, C-terminal / Cilium Assembly / P-loop containing nucleoside triphosphate hydrolase / Kinesin-like protein / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Kinesin motor domain / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Kinesin motor domain signature. / Kinesin motor domain profile. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / MHC class II antigen presentation / Intraflagellar transport / MHC class II antigen presentation / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / RHO GTPases Activate Formins / Hedgehog 'on' state / The role of GTSE1 in G2/M progression after G2 checkpoint / Carboxyterminal post-translational modifications of tubulin / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Insulin processing / RHO GTPases activate KTN1 / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / Kinesins / COPI-mediated anterograde transport / positive regulation of voltage-gated sodium channel activity / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / positive regulation of potassium ion transport / cytoskeleton-dependent intracellular transport / microtubule lateral binding / positive regulation of vesicle fusion / stress granule disassembly / positive regulation of intracellular protein transport / ATP-dependent microtubule motor activity, plus-end-directed / positive regulation of axon guidance / ciliary rootlet / JUN kinase binding / centrosome localization / microtubule motor activity / kinesin complex / microtubule-based movement / regulation of membrane potential / positive regulation of insulin secretion involved in cellular response to glucose stimulus / axon cytoplasm / microtubule-based process / phagocytic vesicle / hippocampus development / axonal growth cone / neuron migration / structural constituent of cytoskeleton / cellular response to interferon-gamma / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / microtubule cytoskeleton / positive regulation of protein localization to plasma membrane / microtubule organizing center / positive regulation of synaptic transmission, GABAergic / axon guidance / microtubule / microtubule binding / vesicle / cadherin binding / GTPase activity / GTP binding / protein heterodimerization activity / perinuclear region of cytoplasm / membrane / ATP binding / identical protein binding / cytosol / cytoplasm / Tubulin alpha-1A chain
Function and homology information
Specimen sourceHomo sapiens (human)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
AuthorsSindelar, C.V. / Downing, K.H.
CitationJournal: J. Cell Biol. / Year: 2007
Title: The beginning of kinesin's force-generating cycle visualized at 9-A resolution.
Authors: Charles V Sindelar / Kenneth H Downing
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 12, 2007 / Release: Jul 8, 2008
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 8, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 18, 2018Structure modelAuthor supporting evidence / Data collectionem_image_scans / em_single_particle_entity / em_software_em_software.image_processing_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1340
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1340
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1340
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: Kinesin heavy chain
A: Tubulin alpha chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,79610
Polyers136,4343
Non-polymers2,3627
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein/peptide , 3 types, 3 molecules KAB

#1: Protein/peptide Kinesin heavy chain / / Ubiquitous kinesin heavy chain / UKHC


Mass: 36405.070 Da / Num. of mol.: 1 / Fragment: K349 Construct of Human Kinesin / Source: (natural) Homo sapiens (human)
Details: The actual construct used in the EM studies is a mutant protein (called cys-lite)
References: UniProt: P33176*PLUS
#2: Protein/peptide Tubulin alpha chain


Mass: 50121.266 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P02550*PLUS
#3: Protein/peptide Tubulin beta chain / Beta tubulin


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

-
Non-polymers , 6 types, 7 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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


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


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

-
Details

Sequence detailsTHE SEQUENCE OF KINESIN (CHAIN K) IN THE SAMPLE INCLUDED MUTATIONS.THE CONSTRUCT IS KNOWN AS ...THE SEQUENCE OF KINESIN (CHAIN K) IN THE SAMPLE INCLUDED MUTATIONS.THE CONSTRUCT IS KNOWN AS CYS-LITE. MODEL CRYSTAL STRUCTURE FOR FITTING THE MAP WAS THE NATIVE SEQUENCE. IN THE CASE OF TUBULIN A AND B (CHAINS A AND B), THE SEQUENCE IN THE SAMPLE WAS DERIVED FROM COW, WHILE THE MODEL USED FOR FITTING THE MAP WAS A PIG PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent IDDetails
1Nucleotide-free kinesin bound to a 13-protofilament microtubuleCOMPLEX0
2Kinesin heavy chain1microtubule associated complex
3Tubulin alpha chain1microtubule
4Tubulin beta chain1microtubule
Buffer solutionpH: 6.8
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE

-
Electron microscopy imaging

MicroscopyMicroscope model: JEOL 4000
Electron gunElectron source: LAB6 / Accelerating voltage: 400 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 4.1 mm
Specimen holderTemperature: 103.15 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 16 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

EM software
IDNameCategory
1Situsmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction was integrated into the back projection process with a customized C program
3D reconstructionMethod: Back projection with integrated CTF correction / Resolution: 9 Å / Number of particles: 150000 / Nominal pixel size: 1 / Actual pixel size: 0.98
Magnification calibration: The magnification was calibrated by assuming a microtubule dimer spacing of 80.0 Angstroms.
Details: Single-particle analysis was employed. / Symmetry type: HELICAL
Atomic model buildingRef space: RECIPROCAL
Atomic model building
IDPDB-ID 3D fitting ID
11JFF1
21BG21
Number of atoms included #LASTProtein: 9112 / Nucleic acid: 0 / Ligand: 152 / Solvent: 0 / Total: 9264

+
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