[English] 日本語
Yorodumi
- PDB-7pkn: Structure of the human CCAN deltaCT complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pkn
TitleStructure of the human CCAN deltaCT complex
Components(Centromere protein ...) x 11
KeywordsCELL CYCLE / Kinetochore / chromosome segregation / centromere
Function / homology
Function and homology information


Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / : / kinetochore organization / metaphase chromosome alignment / kinetochore binding / CENP-A containing chromatin assembly / sex differentiation / chordate embryonic development / negative regulation of epithelial cell apoptotic process ...Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / : / kinetochore organization / metaphase chromosome alignment / kinetochore binding / CENP-A containing chromatin assembly / sex differentiation / chordate embryonic development / negative regulation of epithelial cell apoptotic process / kinetochore assembly / inner kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / NRIF signals cell death from the nucleus / Resolution of Sister Chromatid Cohesion / positive regulation of epithelial cell proliferation / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / kinetochore / centriolar satellite / Separation of Sister Chromatids / actin cytoskeleton / chromosome / cell adhesion / nuclear body / cell division / apoptotic process / regulation of DNA-templated transcription / nucleolus / signal transduction / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / Centromere protein H, C-terminal / Centromere protein Cenp-M ...Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / Centromere protein H, C-terminal / Centromere protein Cenp-M / Centromere protein Cenp-K / Centromere protein H / Centromere protein H (CENP-H) / Centromere protein M (CENP-M) / Centromere-associated protein K / Centromere protein I / Mis6 / Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein O / : / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Centromere protein R / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein I / Centromere protein N / Centromere protein K / Centromere protein O / Centromere protein H / Centromere protein M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMuir, K.W. / Yatskevich, S. / Bellini, D. / Barford, D.
Funding support Germany, 3items
OrganizationGrant numberCountry
Cancer Research UK Germany
Medical Research Council (MRC, United Kingdom) Germany
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Science / Year: 2022
Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford /
Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Centromere protein H
I: Centromere protein I
K: Centromere protein K
L: Centromere protein L
M: Centromere protein M
N: Centromere protein N
O: Centromere protein O
P: Centromere protein P
Q: Centromere protein Q
U: Centromere protein U
R: Centromere protein R


Theoretical massNumber of molelcules
Total (without water)410,97611
Polymers410,97611
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Centromere protein ... , 11 types, 11 molecules HIKLMNOPQUR

#1: Protein Centromere protein H / CENP-H / Interphase centromere complex protein 35


Mass: 28520.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPH, ICEN35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3R5
#2: Protein Centromere protein I / CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / ...CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / Interphase centromere complex protein 19 / Leucine-rich primary response protein 1


Mass: 86820.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI, FSHPRH1, ICEN19, LRPR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92674
#3: Protein Centromere protein K / CENP-K / Interphase centromere complex protein 37 / Protein AF-5alpha / p33


Mass: 31696.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK, ICEN37, FKSG14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS16
#4: Protein Centromere protein L / CENP-L / Interphase centromere complex protein 33


Mass: 39039.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPL, C1orf155, ICEN33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N0S6
#5: Protein Centromere protein M / CENP-M / Interphase centromere complex protein 39 / Proliferation-associated nuclear element protein 1


Mass: 19761.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NSP4
#6: Protein Centromere protein N / CENP-N / Interphase centromere complex protein 32


Mass: 39609.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPN, C16orf60, ICEN32, BM-309 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96H22
#7: Protein Centromere protein O / CENP-O / Interphase centromere complex protein 36


Mass: 33830.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO, ICEN36, MCM21R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BU64
#8: Protein Centromere protein P / CENP-P


Mass: 33210.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IPU0
#9: Protein Centromere protein Q / CENP-Q


Mass: 30648.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ, C6orf139 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7L2Z9
#10: Protein Centromere protein U / CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV ...CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV latent nuclear antigen-interacting protein 1 / MLF1-interacting protein / Polo-box-interacting protein 1


Mass: 47609.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q71F23
#11: Protein Centromere protein R / CENP-R / Beta-3-endonexin / Integrin beta-3-binding protein / Nuclear receptor-interacting factor 3


Mass: 20228.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3BP, CENPR, NRIF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13352

-
Non-polymers , 1 types, 1 molecules

#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human inner kinetochore CCAN / Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 569755 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 187.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002218959
ELECTRON MICROSCOPYf_angle_d0.503925585
ELECTRON MICROSCOPYf_chiral_restr0.03762949
ELECTRON MICROSCOPYf_plane_restr0.0033212
ELECTRON MICROSCOPYf_dihedral_angle_d3.52292446

+
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