[English] 日本語
Yorodumi
- EMDB-6595: Cryo-EM of the C. elegans Ndc80 complex bound to microtubules -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6595
TitleCryo-EM of the C. elegans Ndc80 complex bound to microtubules
Map dataHelical reconstruction of the C. elegans Ndc80 complex bound to microtubules in the presence of the SKA1 complex
Sample
  • Sample: full-length C. elegans Ndc80 complex bound to microtubules
  • Organelle or cellular component: microtubule
  • Protein or peptide: Ndc80
KeywordsKinetochore protein complex
Biological speciesunidentified (others) / Caenorhabditis elegans (invertebrata)
Methodhelical reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsWilson-Kubalek EM / Cheeseman IM / Milligan RA
CitationJournal: Mol Biol Cell / Year: 2016
Title: Structural comparison of the Caenorhabditis elegans and human Ndc80 complexes bound to microtubules reveals distinct binding behavior.
Authors: Elizabeth M Wilson-Kubalek / Iain M Cheeseman / Ronald A Milligan /
Abstract: During cell division, kinetochores must remain tethered to the plus ends of dynamic microtubule polymers. However, the molecular basis for robust kinetochore-microtubule interactions remains poorly ...During cell division, kinetochores must remain tethered to the plus ends of dynamic microtubule polymers. However, the molecular basis for robust kinetochore-microtubule interactions remains poorly understood. The conserved four-subunit Ndc80 complex plays an essential and direct role in generating dynamic kinetochore-microtubule attachments. Here we compare the binding of theCaenorhabditis elegansand human Ndc80 complexes to microtubules at high resolution using cryo-electron microscopy reconstructions. Despite the conserved roles of the Ndc80 complex in diverse organisms, we find that the attachment mode of these complexes for microtubules is distinct. The human Ndc80 complex binds every tubulin monomer along the microtubule protofilament, whereas theC. elegansNdc80 complex binds more tightly to β-tubulin. In addition, theC. elegansNdc80 complex tilts more toward the adjacent protofilament. These structural differences in the Ndc80 complex between different species may play significant roles in the nature of kinetochore-microtubule interactions.
History
DepositionFeb 23, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseMar 23, 2016-
UpdateApr 27, 2016-
Current statusApr 27, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6595.gif

Downloads & links

-
Map

FileDownload / File: emd_6595.map.gz / Format: CCP4 / Size: 16.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of the C. elegans Ndc80 complex bound to microtubules in the presence of the SKA1 complex
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 2.4 / Movie #1: 2.4
Minimum - Maximum-5.49562883 - 15.346900939999999
Average (Standard dev.)0.11449817 (±1.56814516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0100240
Dimensions257157111
Spacing257157111
CellA: 205.67 Å / B: 336.66998 Å / C: 145.40999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z157257111
origin x/y/z0.0000.0000.000
length x/y/z205.670336.670145.410
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS1000240
NC/NR/NS157257111
D min/max/mean-5.49615.3470.114

-
Supplemental data

-
Sample components

-
Entire : full-length C. elegans Ndc80 complex bound to microtubules

EntireName: full-length C. elegans Ndc80 complex bound to microtubules
Components
  • Sample: full-length C. elegans Ndc80 complex bound to microtubules
  • Organelle or cellular component: microtubule
  • Protein or peptide: Ndc80

-
Supramolecule #1000: full-length C. elegans Ndc80 complex bound to microtubules

SupramoleculeName: full-length C. elegans Ndc80 complex bound to microtubules
type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 2

-
Supramolecule #1: microtubule

SupramoleculeName: microtubule / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Macromolecule #1: Ndc80

MacromoleculeName: Ndc80 / type: protein_or_peptide / ID: 1
Details: C. elegans Ndc80 complex was bound to the microtubule in the presence of the SKA1 complex
Recombinant expression: Yes
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / synonym: nematode
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pST39

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 6.8 / Details: 80 mM PIPES, pH 6.8, 1 mM MgCl2, 1 mM EGTA
GridDetails: 400-mesh C-flat grids (Protochips, Inc) containing 2.0 micron holes separated by 2.0 micron spacing
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Method: Blotted back of grid for 3 seconds.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateSep 23, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 1.31 µm / Number real images: 984 / Average electron dose: 40 e/Å2 / Details: Each image is an average of 40 frames.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: CTFIND v3
Final reconstructionApplied symmetry - Helical parameters - Δz: 11.092 Å
Applied symmetry - Helical parameters - Δ&Phi: 23.825 °
Applied symmetry - Helical parameters - Axial symmetry: C15 (15 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: OTHER / Software - Name: EMAN2, FREALIGN, IHRSR
Details: The final map was calculated from two averaged data sets.
DetailsEMAN2 with IHRSR adapted for microtubules with a dimer repeat and FREALIGN was used.

+
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