[English] 日本語
Yorodumi
- PDB-6h8q: Structural basis for Scc3-dependent cohesin recruitment to chromatin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h8q
TitleStructural basis for Scc3-dependent cohesin recruitment to chromatin
Components
  • (DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)- ...) x 3
  • Cohesin subunit SCC3
  • DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
  • Sister chromatid cohesion protein 1
KeywordsCELL CYCLE / Cohesin cell proliferation Scc3 DNA binding
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic 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 ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic 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 / chromosome segregation / G2/M transition of mitotic cell cycle / double-strand break repair / cell division / DNA damage response / chromatin binding / chromatin / apoptotic process / protein kinase binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Cohesin subunit SCC3, C-terminal domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal ...: / Cohesin subunit SCC3, C-terminal domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / 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 / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Cohesin subunit SCC3 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.631 Å
AuthorsLi, Y. / Muir, K. / Panne, D.
CitationJournal: Elife / Year: 2018
Title: Structural basis for Scc3-dependent cohesin recruitment to chromatin.
Authors: Li, Y. / Muir, K. / Bowler, M.W. / Metz, J. / Haering, C.H. / Panne, D.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cohesin subunit SCC3
B: Cohesin subunit SCC3
G: Sister chromatid cohesion protein 1
H: Sister chromatid cohesion protein 1
E: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
C: DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)312,8078
Polymers312,8078
Non-polymers00
Water00
1
A: Cohesin subunit SCC3
G: Sister chromatid cohesion protein 1
E: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)156,4044
Polymers156,4044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-37 kcal/mol
Surface area53700 Å2
MethodPISA
2
B: Cohesin subunit SCC3
H: Sister chromatid cohesion protein 1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)156,4034
Polymers156,4034
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-43 kcal/mol
Surface area53760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)296.240, 110.020, 115.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 4 molecules ABGH

#1: Protein Cohesin subunit SCC3 / Irregular cell behavior protein 1


Mass: 133172.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: IRR1, SCC3, YIL026C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P40541
#2: Protein Sister chromatid cohesion protein 1


Mass: 11583.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q12158

-
DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)- ... , 3 types, 3 molecules EFD

#3: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5861.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5785.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5769.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
DNA chain , 1 types, 1 molecules C

#5: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')


Mass: 5876.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 10% PEG 8000, 0.1M Bis-TRIS, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 20963 / % possible obs: 91.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.9
Reflection shellResolution: 3.6→3.8 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UVK, 4UVL

4uvk

4uvl


Resolution: 3.631→50 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 50.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3185 1093 5.22 %
Rwork0.2835 --
obs0.2854 20930 48.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.631→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14805 1558 0 0 16363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216842
X-RAY DIFFRACTIONf_angle_d0.45123076
X-RAY DIFFRACTIONf_dihedral_angle_d15.1519925
X-RAY DIFFRACTIONf_chiral_restr0.0342683
X-RAY DIFFRACTIONf_plane_restr0.0032610

+
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