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- EMDB-10964: Rod-shaped arm segment of the S.cerevisiae condensin complex in p... -

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Basic information

Entry
Database: EMDB / ID: EMD-10964
TitleRod-shaped arm segment of the S.cerevisiae condensin complex in presence of ATP
Map data
Sample
  • Complex: Rod-shaped arm segment of condensin in presence of ATP
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsMerkel F / Haering CH / Hassler M / Lowe J / Lee BG
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG 681365European Union
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 29, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10964.png

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Map

FileDownload / File: emd_10964.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 90 pix.
= 306. Å		3.4 Å/pix.
x 90 pix.
= 306. Å		3.4 Å/pix.
x 90 pix.
= 306. Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.024102928 - 0.15293168
Average (Standard dev.)-0.00092865905 (±0.009535933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.43.43.4
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z306.000306.000306.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-0.0240.153-0.001

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Supplemental data

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Mask #1

Fileemd_10964_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_10964_half_map_1.map
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Half map: #2

Fileemd_10964_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rod-shaped arm segment of condensin in presence of ATP

EntireName: Rod-shaped arm segment of condensin in presence of ATP
Components
  • Complex: Rod-shaped arm segment of condensin in presence of ATP

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Supramolecule #1: Rod-shaped arm segment of condensin in presence of ATP

SupramoleculeName: Rod-shaped arm segment of condensin in presence of ATP
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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