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

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Basic information

Entry
Database: PDB / ID: 5oqn
TitleCrystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex bound to DNA (short kleisin loop)
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 / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / 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 / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / 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: 3.15 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 1.2Dec 27, 2017Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Mar 28, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.details
Revision 1.4Jan 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')


Theoretical massNumber of molelcules
Total (without water)125,8724
Polymers125,8724
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-59 kcal/mol
Surface area49120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.149, 116.220, 155.518
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: 99715.875 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: 15124.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 384-529 loop deletion: 418-444
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)

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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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 280 K / Method: vapor diffusion
Details: 4% (w/v) PEG 4000, 0.05 M Na citrate pH 5.6, 5 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→48.68 Å / Num. obs: 28612 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.059 / Net I/σ(I): 8.4
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4129 / CC1/2: 0.287 / Rpim(I) all: 0.401 / % 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: 5OQP

5oqp


Resolution: 3.15→47.343 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2805 1999 6.99 %
Rwork0.2494 --
obs0.2516 28612 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→47.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7380 732 0 0 8112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038321
X-RAY DIFFRACTIONf_angle_d0.57111389
X-RAY DIFFRACTIONf_dihedral_angle_d18.9734956
X-RAY DIFFRACTIONf_chiral_restr0.0371316
X-RAY DIFFRACTIONf_plane_restr0.0031327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.22880.42291400.38471867X-RAY DIFFRACTION100
3.2288-3.31610.40651410.391882X-RAY DIFFRACTION100
3.3161-3.41360.38821410.35711867X-RAY DIFFRACTION100
3.4136-3.52380.38821400.33091867X-RAY DIFFRACTION100
3.5238-3.64970.371410.33081875X-RAY DIFFRACTION100
3.6497-3.79570.33561410.30671866X-RAY DIFFRACTION100
3.7957-3.96840.36851420.26711896X-RAY DIFFRACTION100
3.9684-4.17750.29551420.2421891X-RAY DIFFRACTION100
4.1775-4.4390.27091430.22431897X-RAY DIFFRACTION100
4.439-4.78150.24981410.22431878X-RAY DIFFRACTION100
4.7815-5.26210.24521440.21841921X-RAY DIFFRACTION100
5.2621-6.02220.29631430.25251910X-RAY DIFFRACTION100
6.0222-7.58230.28681470.25771946X-RAY DIFFRACTION100
7.5823-47.34850.18971530.17722050X-RAY DIFFRACTION100

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