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- EMDB-13785: Cryo-EM map of clamped S.cerevisiae condensin-DNA complex (pentam... -

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Basic information

Entry
Database: EMDB / ID: EMD-13785
TitleCryo-EM map of clamped S.cerevisiae condensin-DNA complex (pentamer dataset)
Map data
Sample
  • Complex: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
Keywordscondensin / SMC / CELL CYCLE
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLee B-G / Rhodes J / Lowe J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust218621/Z/19/Z United Kingdom
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Clamping of DNA shuts the condensin neck gate.
Authors: Byung-Gil Lee / James Rhodes / Jan Löwe /
Abstract: SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex ...SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolyzed. The DNA is clamped within a compartment that has been reported previously in other structural maintenance of chromosomes (SMC) complexes, including Rad50, cohesin, and MukBEF. With the caveat of important differences, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolyzing ATP and translocating DNA.
History
DepositionOct 26, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13785.png

Downloads & links

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Map

FileDownload / File: emd_13785.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 162 pix.
= 174.96 Å		1.08 Å/pix.
x 162 pix.
= 174.96 Å		1.08 Å/pix.
x 162 pix.
= 174.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.021303039 - 2.084454
Average (Standard dev.)0.0075957184 (±0.06140235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions162162162
Spacing162162162
CellA=B=C: 174.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3

EntireName: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
Components
  • Complex: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3

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Supramolecule #1: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3

SupramoleculeName: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 515 kDa/nm

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45112
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL

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