[English] 日本語
Yorodumi
- EMDB-2533: Electron cryo-microscopy of microtubule-bound human kinesin-5 mot... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 2533
TitleElectron cryo-microscopy of microtubule-bound human kinesin-5 motor domain in the ADP.AlFx state.
Map dataReconstruction of microtubule-bound human kinesin-5 motor domain in presence of ADP.AlFx (ATP hydrolysis transition state)
Sample13-protofilament microtubule-bound human kinesin-5 motor domain with ADP.AlFx:
TUBULIN ALPHA-1D CHAIN / TUBULIN BETA-2B CHAIN / Kinesin-5 motor domain
Keywordscryo-electron microscopy / kinesins / mechanochemistry / microtubules / mitosis
Function / homologyKinesin motor domain, conserved site / Tubulin/FtsZ family, GTPase domain / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / RHO GTPases activate IQGAPs / Tubulin, C-terminal ...Kinesin motor domain, conserved site / Tubulin/FtsZ family, GTPase domain / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / RHO GTPases activate IQGAPs / Tubulin, C-terminal / Kinesin-associated microtubule-binding domain / P-loop containing nucleoside triphosphate hydrolase / Kinesin-like protein / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain / Kinesin motor domain / Tubulin C-terminal domain / Kinesin-associated microtubule-binding / 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 / MHC class II antigen presentation / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Recruitment of NuMA to mitotic centrosomes / Recycling pathway of L1 / Hedgehog 'off' state / Alpha tubulin / Tubulin / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / Kinesins / Carboxyterminal post-translational modifications of tubulin / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / Cilium Assembly / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / Hedgehog 'on' state / RHO GTPases Activate Formins / ATP-dependent microtubule motor activity, plus-end-directed / positive regulation of axon guidance / regulation of mitotic centrosome separation / mitotic centrosome separation / kinesin complex / retrograde vesicle-mediated transport, Golgi to ER / mitotic spindle assembly / microtubule-based process / spindle organization / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule motor activity / mitotic spindle / mitotic spindle organization / microtubule-based movement / neuron migration / structural constituent of cytoskeleton / chromosome segregation / microtubule cytoskeleton / spindle / mitotic cell cycle / spindle pole / protein-containing complex binding / microtubule / microtubule binding / GTPase activity / cell division / GTP binding / protein kinase binding / protein heterodimerization activity / membrane / ATP binding / cytosol / cytoplasm / Kinesin-like protein KIF11 / Tubulin alpha-1D chain / Tubulin beta-2B chain
Function and homology information
SourceBos taurus (cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 9.2 Å resolution
AuthorsGoulet A / Major J / Jun Y / Gross SP / Rosenfeld SS / Moores CA
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family.
Authors: Adeline Goulet / Jennifer Major / Yonggun Jun / Steven P Gross / Steven S Rosenfeld / Carolyn A Moores
Validation ReportPDB-ID: 4ck6

SummaryFull report
PDB-ID: 4ck7

SummaryFull report
About validation report
DateDeposition: Dec 30, 2013 / Header (metadata) release: Jan 15, 2014 / Map release: Feb 5, 2014 / Last update: Feb 12, 2014

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4ck6
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4ck7
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_2533.map.gz (map file in CCP4 format, 199 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
37 pix
2.8 Å/pix.
= 103.6 Å
37 pix
2.8 Å/pix.
= 103.6 Å
37 pix
2.8 Å/pix.
= 103.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:1.1 (by author), 1.1 (movie #1):
Minimum - Maximum-7.90483379 - 9.52293491
Average (Standard dev.)0.2909551 (1.94621992)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions373737
Origin7545128
Limit11181164
Spacing373737
CellA=B=C: 103.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z373737
origin x/y/z0.0000.0000.000
length x/y/z103.600103.600103.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS4575128
NC/NR/NS373737
D min/max/mean-7.9059.5230.291

-
Supplemental data

-
Sample components

-
Entire 13-protofilament microtubule-bound human kinesin-5 motor domain w...

EntireName: 13-protofilament microtubule-bound human kinesin-5 motor domain with ADP.AlFx
Number of components: 3
Oligomeric State: 13-protofilament microtubule with one kineisn-5 motor domain bound every tubulin heterodimers

-
Component #1: protein, TUBULIN ALPHA-1D CHAIN

ProteinName: TUBULIN ALPHA-1D CHAIN / a.k.a: ALPHA TUBULIN / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (natural)Organ or tissue: brain
External referencesUniProt: Tubulin alpha-1D chain

-
Component #2: protein, TUBULIN BETA-2B CHAIN

ProteinName: TUBULIN BETA-2B CHAIN / a.k.a: BETA TUBULIN / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (natural)Organ or tissue: brain
External referencesUniProt: Tubulin beta-2B chain

-
Component #3: protein, Kinesin-5 motor domain

ProteinName: Kinesin-5 motor domain / Details: cys-lite mutant containing the substitution T126C / Recombinant expression: Yes
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pet21a

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 80 mM PIPES, 5 mM MgCl2, 1 mM EGTA, 2 mM ADPAlFx
pH: 6.8
Support film400 mesh holey carbon grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Method: chamber at 24 degrees C, 100% humidity, blot 3.5 sec

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Mar 10, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2500 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 125 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 10692
Details: The particles were selected along individual microtubules.
3D reconstructionSoftware: SPIDER, FREALIGN / CTF correction: FREALIGN
Details: Approximately 139,000 asymmetric units were averaged in the final reconstruction.
Resolution: 9.2 Å / Resolution method: FSC 0.5, semi-independent

-
Atomic model buiding

Modeling #1Software: Chimera, FlexEM / Refinement protocol: flexible / Target criteria: cross-correlation / Refinement space: REAL
Input PDB model: 3HQD
Chain ID: C
Modeling #2Software: Chimera / Refinement protocol: flexible / Target criteria: cross-correlation / Refinement space: REAL
Input PDB model: 1JFF
Chain ID: A, B
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