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- PDB-6yvv: Condensin complex from S.cerevisiae ATP-free apo bridged state -

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Basic information

Entry
Database: PDB / ID: 6yvv
TitleCondensin complex from S.cerevisiae ATP-free apo bridged state
Components
  • Condensin complex subunit 1,Ycs4
  • Condensin complex subunit 2,Brn1
  • Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2
  • Structural maintenance of chromosomes protein 4
KeywordsCELL CYCLE / essential for the functional organization of genomes
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 / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome condensation / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy / synaptonemal complex assembly / condensed chromosome, centromeric region / mitotic chromosome condensation / chromosome condensation / silent mating-type cassette heterochromatin formation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / condensed chromosome / double-stranded DNA binding / histone binding / cell division / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Condensin subunit 1 / Condensin complex subunit 1, N-terminal / non-SMC mitotic condensation complex subunit 1, N-term / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein ...Condensin subunit 1 / Condensin complex subunit 1, N-terminal / non-SMC mitotic condensation complex subunit 1, N-term / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Condensin complex subunit 2 / Structural maintenance of chromosomes protein 2 / Condensin complex subunit 1 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsLee, B.-G. / Cawood, C. / Gutierrez-Escribano, P. / Nakane, T. / Merkel, F. / Hassler, M. / Haering, C.H. / Aragon, L. / Lowe, J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC-A652-5PY00 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.
Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol ...Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol Bravo / Takanori Nakane / Juri Rappsilber / Luis Aragon / Martin Beck / Jan Löwe / Christian H Haering /
Abstract: Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The ...Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2
B: Structural maintenance of chromosomes protein 4
C: Condensin complex subunit 2,Brn1
D: Condensin complex subunit 1,Ycs4


Theoretical massNumber of molelcules
Total (without water)519,0664
Polymers519,0664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10970 Å2
ΔGint-70 kcal/mol
Surface area113660 Å2
MethodPISA

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Components

#1: Protein Structural maintenance of chromosomes protein 2,Structural maintenance of chromosomes protein 2 / DA-box protein SMC2


Mass: 134806.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SMC2, YFR031C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38989
#2: Protein Structural maintenance of chromosomes protein 4


Mass: 162435.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SMC4, YLR086W, L9449.5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12267
#3: Protein Condensin complex subunit 2,Brn1 / Barren homolog / CAPH homolog


Mass: 87940.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: BRN1, YBL097W, YBL0830 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38170
#4: Protein Condensin complex subunit 1,Ycs4 / XCAP-D2 homolog


Mass: 133882.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: YCS4, LOC7, YLR272C, L8479.14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06156

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Condensin / Type: COMPLEX
Details: complex of 5 protein subunits: Smc2; Smc4; Brn1; Ycs4; Ycg1
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 500 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer componentName: Tris
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 100 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10000
EM imaging opticsEnergyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
3SerialEMimage acquisition
5GctfCTF correction
8UCSF Chimeramodel fitting
10RELIONmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
14RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24593 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
14RSI

4rsi

A4RSI1
24RSI

4rsi

B4RSI1
36QJ2

6qj2

A6QJ22
46QJ2

6qj2

B6QJ22
56CJ3

6cj3

A6CJ33
66C63

6c63

A6C634
76Q6E

6q6e

6Q6E5
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00115624
ELECTRON MICROSCOPYf_angle_d0.46421067
ELECTRON MICROSCOPYf_dihedral_angle_d16.3862113
ELECTRON MICROSCOPYf_chiral_restr0.0372518
ELECTRON MICROSCOPYf_plane_restr0.0032673

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