[English] 日本語
Yorodumi
- EMDB-5166: 3D reconstruction of a microtubule decorated with monomeric human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5166
Title3D reconstruction of a microtubule decorated with monomeric human kinesin (K349 construct) having AMPPNP bound in the nucleotide pocket.
Map data3D reconstruction of a microtubule decorated with monomeric human kinesin (K349 construct) with AMPPNP bound in the nucleotide pocket.
Sample
  • Sample: Microtubule decorated with monomeric human kinesin (K349 construct) having AMPPNP bound in the nucleotide pocket.
  • Protein or peptide: K349
  • Protein or peptide: Microtubule
Keywordskinesin / microtubule / atpase / molecular motor / myosin / mechanism / motility / cytoskeleton
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsSindelar CV / Downing KH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: An atomic-level mechanism for activation of the kinesin molecular motors.
Authors: Charles V Sindelar / Kenneth H Downing /
Abstract: Kinesin cytoskeletal motors convert the energy of ATP hydrolysis into stepping movement along microtubules. A partial model of this process has been derived from crystal structures, which show that ...Kinesin cytoskeletal motors convert the energy of ATP hydrolysis into stepping movement along microtubules. A partial model of this process has been derived from crystal structures, which show that movement of the motor domain relative to its major microtubule binding element, the switch II helix, is coupled to docking of kinesin's neck linker element along the motor domain. This docking would displace the cargo in the direction of travel and so contribute to a step. However, the crystal structures do not reveal how ATP binding and hydrolysis govern this series of events. We used cryoelectron microscopy to derive 8-9 A-resolution maps of four nucleotide states encompassing the microtubule-attached kinetic cycle of a kinesin motor. The exceptionally high quality of these maps allowed us to build in crystallographically determined conformations of kinesin's key subcomponents, yielding novel arrangements of kinesin's switch II helix and nucleotide-sensing switch loops. The resulting atomic models reveal a seesaw mechanism in which the switch loops, triggered by ATP binding, propel their side of the motor domain down and thereby elicit docking of the neck linker on the opposite side of the seesaw. Microtubules engage the seesaw mechanism by stabilizing the formation of extra turns at the N terminus of the switch II helix, which then serve as an anchor for the switch loops as they modulate the seesaw angle. These observations explain how microtubules activate kinesin's ATP-sensing machinery to promote cargo displacement and inform the mechanism of kinesin's ancestral relative, myosin.
History
DepositionFeb 3, 2010-
Header (metadata) releaseFeb 23, 2010-
Map releaseFeb 23, 2010-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.051
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.051
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5166.map.gz / Format: CCP4 / Size: 165 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of a microtubule decorated with monomeric human kinesin (K349 construct) with AMPPNP bound in the nucleotide pocket.
Voxel sizeX=Y=Z: 2.1167 Å
Density
Contour LevelBy AUTHOR: 0.051 / Movie #1: 0.051
Minimum - Maximum-0.0604785 - 0.171181
Average (Standard dev.)0.0121831 (±0.0332382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-15497
Dimensions353535
Spacing353535
CellA=B=C: 74.0845 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.11671428571432.11671428571432.1166857142857
M x/y/z353535
origin x/y/z0.0000.0000.000
length x/y/z74.08574.08574.084
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS49-157
NC/NR/NS353535
D min/max/mean-0.0600.1710.012

-
Supplemental data

-
Sample components

-
Entire : Microtubule decorated with monomeric human kinesin (K349 construc...

EntireName: Microtubule decorated with monomeric human kinesin (K349 construct) having AMPPNP bound in the nucleotide pocket.
Components
  • Sample: Microtubule decorated with monomeric human kinesin (K349 construct) having AMPPNP bound in the nucleotide pocket.
  • Protein or peptide: K349
  • Protein or peptide: Microtubule

-
Supramolecule #1000: Microtubule decorated with monomeric human kinesin (K349 construc...

SupramoleculeName: Microtubule decorated with monomeric human kinesin (K349 construct) having AMPPNP bound in the nucleotide pocket.
type: sample / ID: 1000 / Number unique components: 2

-
Macromolecule #1: K349

MacromoleculeName: K349 / type: protein_or_peptide / ID: 1 / Name.synonym: Monomeric human kinesin construct / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Macromolecule #2: Microtubule

MacromoleculeName: Microtubule / type: protein_or_peptide / ID: 2 / Name.synonym: Microtubule / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8 / Details: 25mM Pipes, 25mM NaCl, 2mM MgCl2, 1mM EGTA
GridDetails: 300 mesh copper grid with homemade holey carbon
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homemade

-
Electron microscopy

MicroscopeJEOL 4000EX
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 105 K
DateJan 21, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 98 / Average electron dose: 15 e/Å2 / Bits/pixel: 16

-
Image processing

CTF correctionDetails: done within FREALIGN
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER,FREALIGN
Details: Approximately 190,000 asymmetric units were averaged in the final reconstruction.

-
Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Regions in the crystal structure whose structure were found to differ from the EM map were excluded from the fitting procedure. These regions corresponded to the switch loops, helices alpha 3 and alpha 4 (switch II helix), and the neck linker.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation

+
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