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- PDB-5oqp: Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcom... -

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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 / tRNA gene clustering / meiotic chromosome condensation / 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 / tRNA gene clustering / meiotic chromosome condensation / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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