[English] 日本語
Yorodumi
- PDB-5oqp: Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oqp
TitleCrystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex bound to DNA (crystal form I)
Components
  • Condensin complex subunit 2
  • Condensin complex subunit 3
  • DNA (5'-D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3')
KeywordsCELL CYCLE / kleisin / HEAT repeat / DNA-binding / SMC complex
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation / mitotic sister chromatid segregation / condensed chromosome / cell division / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Condensin complex subunit 2 / Condensin complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsKschonsak, M. / Hassler, M. / Haering, C.H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation5853/2 Germany
European Research CouncilERC-2015-CoG 681365
CitationJournal: Cell / Year: 2017
Title: Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes.
Authors: Kschonsak, M. / Merkel, F. / Bisht, S. / Metz, J. / Rybin, V. / Hassler, M. / Haering, C.H.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Condensin complex subunit 3
B: Condensin complex subunit 2
C: DNA (5'-D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0306
Polymers128,6964
Non-polymers3342
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-67 kcal/mol
Surface area47890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.140, 114.833, 155.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Condensin complex subunit 3 / CAPG homolog


Mass: 99529.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: loop deletion; 499-555
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: YCG1, YCS5, YDR325W / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q06680
#2: Protein Condensin complex subunit 2 / Barren homolog / CAPH homolog


Mass: 18134.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 384-529
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: BRN1, YBL097W, YBL0830 / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: P38170
#3: DNA chain DNA (5'-D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3')


Mass: 5515.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 280 K / Method: vapor diffusion
Details: 4% (w/v) PEG 4000 0.05 M Na citrate pH 6.6 5 mM MgSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.98→47.171 Å / Num. obs: 29952 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.084 / Net I/σ(I): 8.5
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4290 / CC1/2: 0.565 / Rpim(I) all: 0.572 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQQ

5oqq


Resolution: 2.98→47.171 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 2000 6.68 %
Rwork0.2185 --
obs0.2214 29952 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→47.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7317 732 21 0 8070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038278
X-RAY DIFFRACTIONf_angle_d0.54711327
X-RAY DIFFRACTIONf_dihedral_angle_d19.5924925
X-RAY DIFFRACTIONf_chiral_restr0.0381308
X-RAY DIFFRACTIONf_plane_restr0.0031315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.05450.38291390.33921951X-RAY DIFFRACTION100
3.0545-3.13710.36651410.32071956X-RAY DIFFRACTION100
3.1371-3.22940.35921410.31211969X-RAY DIFFRACTION100
3.2294-3.33360.33891410.3061983X-RAY DIFFRACTION100
3.3336-3.45270.36821400.2841951X-RAY DIFFRACTION100
3.4527-3.59090.31591420.26051987X-RAY DIFFRACTION100
3.5909-3.75430.28131410.23941964X-RAY DIFFRACTION100
3.7543-3.95210.27751430.21991992X-RAY DIFFRACTION100
3.9521-4.19960.26271420.19311998X-RAY DIFFRACTION100
4.1996-4.52360.23021420.18221981X-RAY DIFFRACTION100
4.5236-4.97840.21451430.17342014X-RAY DIFFRACTION100
4.9784-5.69770.2341450.19542017X-RAY DIFFRACTION100
5.6977-7.17440.2341460.22692047X-RAY DIFFRACTION100
7.1744-47.17640.19891540.17062142X-RAY DIFFRACTION100

+
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