[English] 日本語
Yorodumi
- PDB-7qpg: Human RZZ kinetochore corona complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qpg
TitleHuman RZZ kinetochore corona complex.
Components
  • Centromere/kinetochore protein zw10 homolog
  • Kinetochore-associated protein 1
  • Protein zwilch homolog
KeywordsCELL CYCLE / Kinetochore / centromere / chromosome segregation / mitosis
Function / homology
Function and homology information


protein localization to kinetochore involved in kinetochore assembly / RZZ complex / Dsl1/NZR complex / kinetochore microtubule / centromeric DNA binding / regulation of attachment of spindle microtubules to kinetochore / regulation of exit from mitosis / protein localization to kinetochore / COPI-dependent Golgi-to-ER retrograde traffic / mitotic metaphase chromosome alignment ...protein localization to kinetochore involved in kinetochore assembly / RZZ complex / Dsl1/NZR complex / kinetochore microtubule / centromeric DNA binding / regulation of attachment of spindle microtubules to kinetochore / regulation of exit from mitosis / protein localization to kinetochore / COPI-dependent Golgi-to-ER retrograde traffic / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / Golgi organization / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / endoplasmic reticulum to Golgi vesicle-mediated transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / lipid droplet / bioluminescence / meiotic cell cycle / generation of precursor metabolites and energy / RHO GTPases Activate Formins / kinetochore / small GTPase binding / spindle pole / Separation of Sister Chromatids / protein transport / actin cytoskeleton / protein-containing complex assembly / cell division / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RZZ complex, subunit Zw10 / RZZ complex, subunit KNTC1/ROD, C-terminal / Centromere/kinetochore Zw10 N-terminal / Rough deal protein C-terminal region / RZZ complex, subunit Zwilch / RZZ complex, subunit zwilch / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Centromere/kinetochore protein zw10 homolog / Kinetochore-associated protein 1 / Protein zwilch homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsRaisch, T. / Ciossani, G. / d'Amico, E. / Cmetowski, V. / Carmignani, S. / Maffini, S. / Merino, F. / Wohlgemuth, S. / Vetter, I.R. / Raunser, S. / Musacchio, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: EMBO J / Year: 2022
Title: Structure of the RZZ complex and molecular basis of Spindly-driven corona assembly at human kinetochores.
Authors: Tobias Raisch / Giuseppe Ciossani / Ennio d'Amico / Verena Cmentowski / Sara Carmignani / Stefano Maffini / Felipe Merino / Sabine Wohlgemuth / Ingrid R Vetter / Stefan Raunser / Andrea Musacchio /
Abstract: In metazoans, a ≈1 megadalton (MDa) multiprotein complex comprising the dynein-dynactin adaptor Spindly and the ROD-Zwilch-ZW10 (RZZ) complex is the building block of a fibrous biopolymer, the ...In metazoans, a ≈1 megadalton (MDa) multiprotein complex comprising the dynein-dynactin adaptor Spindly and the ROD-Zwilch-ZW10 (RZZ) complex is the building block of a fibrous biopolymer, the kinetochore fibrous corona. The corona assembles on mitotic kinetochores to promote microtubule capture and spindle assembly checkpoint (SAC) signaling. We report here a high-resolution cryo-EM structure that captures the essential features of the RZZ complex, including a farnesyl-binding site required for Spindly binding. Using a highly predictive in vitro assay, we demonstrate that the SAC kinase MPS1 is necessary and sufficient for corona assembly at supercritical concentrations of the RZZ-Spindly (RZZS) complex, and describe the molecular mechanism of phosphorylation-dependent filament nucleation. We identify several structural requirements for RZZS polymerization in rings and sheets. Finally, we identify determinants of kinetochore localization and corona assembly of Spindly. Our results describe a framework for the long-sought-for molecular basis of corona assembly on metazoan kinetochores.
History
DepositionJan 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 27, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 11, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-14120
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-14120
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein zwilch homolog
C: Protein zwilch homolog
R: Kinetochore-associated protein 1
S: Kinetochore-associated protein 1
W: Centromere/kinetochore protein zw10 homolog
X: Centromere/kinetochore protein zw10 homolog


Theoretical massNumber of molelcules
Total (without water)872,0796
Polymers872,0796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43430 Å2
ΔGint-177 kcal/mol
Surface area348130 Å2

-
Components

#1: Protein Protein zwilch homolog / hZwilch


Mass: 67293.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZWILCH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H900
#2: Protein Kinetochore-associated protein 1 / Rough deal homolog / HsROD / Rod / hRod


Mass: 279805.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DS885_16260, KNTC1, KIAA0166 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A366VY15, UniProt: P50748
#3: Protein Centromere/kinetochore protein zw10 homolog


Mass: 88940.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZW10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O43264

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RZZ complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191979 / Symmetry type: POINT

+
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://pdbjlvh1.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