[English] 日本語
Yorodumi
- EMDB-4581: Structure of inner kinetochore CCAN complex with mask1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4581
TitleStructure of inner kinetochore CCAN complex with mask1
Map data
SampleInner kinetochore CCAN complex:
(Inner kinetochore subunit ...) x 8
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex / COMA complex / establishment of meiotic sister chromatid cohesion / maintenance of meiotic sister chromatid cohesion / centromere complex assembly / meiotic sister chromatid segregation / attachment of spindle microtubules to kinetochore / ascospore formation / establishment of mitotic sister chromatid cohesion ...negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex / COMA complex / establishment of meiotic sister chromatid cohesion / maintenance of meiotic sister chromatid cohesion / centromere complex assembly / meiotic sister chromatid segregation / attachment of spindle microtubules to kinetochore / ascospore formation / establishment of mitotic sister chromatid cohesion / condensed nuclear chromosome outer kinetochore / protein localization to chromosome, centromeric region / kinetochore assembly / condensed nuclear chromosome kinetochore / spindle pole body / protein localization to kinetochore / condensed chromosome kinetochore / mitotic spindle assembly checkpoint / kinetochore / chromosome segregation / meiotic cell cycle / cell division / structural molecule activity / nucleus / cytoplasm
Centromere protein Chl4/mis15/CENP-N / Centromere protein O / Cenp-O kinetochore centromere component / Cnl2/NKP2 family protein / Kinetochore protein CHL4 like / Kinetochore subunit Nkp2/Cnl2
Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsYan K / Yang J / Zhang Z / McLaughlin SH / Chang L / Fasci D / Heck AJR / Barford D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
European CommissionINFRAIA project Epic-XS (Project 823839)
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome.
Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford /
Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
Validation ReportPDB-ID: 6qlf

SummaryFull reportAbout validation report
History
DepositionJan 31, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseOct 2, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6qlf
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4581.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 348.8 Å
1.09 Å/pix.
x 320 pix.
= 348.8 Å
1.09 Å/pix.
x 320 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.16614649 - 0.25293982
Average (Standard dev.)0.00014513815 (±0.0034088057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1660.2530.000

-
Supplemental data

-
Sample components

+
Entire Inner kinetochore CCAN complex

EntireName: Inner kinetochore CCAN complex / Number of components: 9

+
Component #1: protein, Inner kinetochore CCAN complex

ProteinName: Inner kinetochore CCAN complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #2: protein, Inner kinetochore subunit IML3

ProteinName: Inner kinetochore subunit IML3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.093223 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #3: protein, Inner kinetochore subunit CHL4

ProteinName: Inner kinetochore subunit CHL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.538566 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #4: protein, Inner kinetochore subunit MCM21

ProteinName: Inner kinetochore subunit MCM21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.028879 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #5: protein, Inner kinetochore subunit CTF19

ProteinName: Inner kinetochore subunit CTF19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.841113 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #6: protein, Inner kinetochore subunit OKP1

ProteinName: Inner kinetochore subunit OKP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.427246 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #7: protein, Inner kinetochore subunit AME1

ProteinName: Inner kinetochore subunit AME1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.081246 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #8: protein, Inner kinetochore subunit NKP1

ProteinName: Inner kinetochore subunit NKP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.006451 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #9: protein, Inner kinetochore subunit NKP2

ProteinName: Inner kinetochore subunit NKP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.877033 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 465029
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. 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

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