[English] 日本語
Yorodumi
- PDB-6qpq: The structure of the cohesin head module elucidates the mechanism... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qpq
TitleThe structure of the cohesin head module elucidates the mechanism of ring opening
Components
  • Sister chromatid cohesion protein 1
  • Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
KeywordsCELL CYCLE / Cohesin / cell division / genome regulation / sister chromatid cohesion / SMC / kleisin
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / double-strand break repair / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge ...Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Structural maintenance of chromosomes protein / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, Y. / Muir, K.W. / Panne, D.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening.
Authors: Kyle W Muir / Yan Li / Felix Weis / Daniel Panne /
Abstract: Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring- ...Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
B: Sister chromatid cohesion protein 1
C: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
D: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)230,4724
Polymers230,4724
Non-polymers00
Water6,179343
1
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
B: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)115,2362
Polymers115,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-17 kcal/mol
Surface area24870 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
D: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)115,2362
Polymers115,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-18 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.752, 111.130, 166.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein


Mass: 51883.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0066330 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGH3
#2: Protein Sister chromatid cohesion protein 1


Mass: 63352.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12158
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 30% PEG300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→45.7 Å / Num. obs: 82453 / % possible obs: 98.8 % / Redundancy: 4.5 % / Net I/σ(I): 13.36
Reflection shellResolution: 2.14→2.27 Å

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.7 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs84151 98.8 %
Refinement stepCycle: LAST / Resolution: 2.1→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 0 343 8091

+
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