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- PDB-6qj4: Crystal structure of the C. thermophilum condensin Ycs4-Brn1 subc... -

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Basic information

Entry
Database: PDB / ID: 6qj4
TitleCrystal structure of the C. thermophilum condensin Ycs4-Brn1 subcomplex bound to the Smc4 ATPase head in complex with the C-terminal domain of Brn1
Components
  • (Condensin complex subunit 2) x 2
  • Brn1
  • Condensin complex subunit 1,Condensin complex subunit 1,Condensin complex subunit 1
  • Uncharacterized protein,Uncharacterized protein
KeywordsCELL CYCLE / condensin / SMC complex / ATPase / chromosome condensation / loop extrusion
Function / homology
Function and homology information


condensin complex / mitotic chromosome condensation / chromosome organization / chromosome segregation / mitotic cell cycle / chromosome / cell division / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding ...condensin complex / mitotic chromosome condensation / chromosome organization / chromosome segregation / mitotic cell cycle / chromosome / cell division / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes 4, ABC domain, eukaryotic / Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / Condensin complex subunit 2/barren ...Structural maintenance of chromosomes 4, ABC domain, eukaryotic / Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / Condensin complex subunit 2/barren / Condensin complex subunit 2 / 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 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 4 / Condensin complex subunit 1 / Condensin complex subunit 2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.8 Å
AuthorsHassler, M. / Haering, C.H. / Kschonsak, M.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2015-CoG 681365
CitationJournal: Mol.Cell / Year: 2019
Title: Structural Basis of an Asymmetric Condensin ATPase Cycle.
Authors: Hassler, M. / Shaltiel, I.A. / Kschonsak, M. / Simon, B. / Merkel, F. / Tharichen, L. / Bailey, H.J. / Macosek, J. / Bravo, S. / Metz, J. / Hennig, J. / Haering, C.H.
History
DepositionJan 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 1,Condensin complex subunit 1,Condensin complex subunit 1
B: Condensin complex subunit 2
C: Uncharacterized protein,Uncharacterized protein
D: Brn1
E: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)212,6405
Polymers212,6405
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-53 kcal/mol
Surface area81920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.405, 82.378, 177.834
Angle α, β, γ (deg.)90.000, 98.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Condensin complex subunit 1,Condensin complex subunit 1,Condensin complex subunit 1 /


Mass: 128880.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0049230 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SB82
#2: Protein Condensin complex subunit 2 /


Mass: 21545.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053810 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SBJ6
#3: Protein Uncharacterized protein,Uncharacterized protein


Mass: 44726.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0017120 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S2G2
#4: Protein/peptide Brn1


Mass: 1975.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli)
#5: Protein Condensin complex subunit 2 /


Mass: 15511.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053810 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SBJ6

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS-HCl pH 8.5, 8 % PEG 8,000, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 5.5→175.756 Å / Num. all: 7830 / Num. obs: 7830 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rpim(I) all: 0.079 / Rrim(I) all: 0.145 / Rsym value: 0.121 / Net I/av σ(I): 5.7 / Net I/σ(I): 8.1 / Num. measured all: 25779
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
5.5-5.83.51.3590.511470.851.6081.35999.6
5.8-6.153.41.10.710980.6931.3051.199.3
6.15-6.573.40.7081.110310.4530.8440.70899.1
6.57-7.13.20.4271.79240.280.5140.42796.5
7.1-7.783.40.2133.58840.1370.2550.21397.9
7.78-8.73.40.1096.37720.0710.130.10998.8
8.7-10.043.10.05710.56990.0390.0690.05796.4
10.04-12.330.04415.45730.0310.0540.04494.1
12.3-17.3930.037194600.0250.0450.03795
17.39-47.7432.80.0322.22420.0210.0370.0388.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QJ2 and 6QJ3

6qj2

6qj3


Resolution: 5.8→47.743 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3015 296 4.45 %
Rwork0.2919 6359 -
obs0.2926 6655 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 329.7 Å2 / Biso mean: 210.4145 Å2 / Biso min: 128.15 Å2
Refinement stepCycle: final / Resolution: 5.8→47.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10778 0 0 0 10778
Num. residues----1412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.8001-7.30340.40111490.39583179332898
7.3034-47.74450.27151470.26163180332795

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