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- EMDB-10948: Condensin complex from S.cerevisiae ATP-free apo non-engaged stat... -

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Basic information

Entry
Database: EMDB / ID: EMD-10948
TitleCondensin complex from S.cerevisiae ATP-free apo non-engaged state: focused refinement on head segment
Map data
Sample
  • Complex: Condensin
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLee B-G / Cawood C / Gutierrez-Escribano P / Nakane T / Merkel F / Hassler M / Haering CH / Aragon L / Lowe J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Medical Research Council (MRC, United Kingdom)MC-A652-5PY00 United Kingdom
Wellcome Trust202754/Z/16/Z 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, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10948.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.02267333 - 0.057040356
Average (Standard dev.)0.00005004669 (±0.0009062511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 456.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0230.0570.000

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Supplemental data

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Sample components

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Entire : Condensin

EntireName: Condensin
Components
  • Complex: Condensin

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Supramolecule #1: Condensin

SupramoleculeName: Condensin / type: complex / ID: 1 / Parent: 0
Details: complex of 5 protein subunits: Smc2; Smc4; Brn1; Ycs4; Ycg1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 500 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Component - Name: Tris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10000 / Average exposure time: 10.0 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: NONE / Details: Ab initio
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 576016

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Atomic model buiding 1

Initial model
PDB IDChain

chain_id: A

chain_id: B

chain_id: A

chain_id: B

chain_id: A

chain_id: A

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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