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- EMDB-13950: S.c. Condensin peripheral Ycg1 subcomplex bound to DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-13950
TitleS.c. Condensin peripheral Ycg1 subcomplex bound to DNA
Map datacryoEM half map 1 of S.c. condensin peripheral Ycg1 complex bound to DNA
Sample
  • Complex: S.c. Condensin peripheral Ycg1 complex bound to DNA
    • Protein or peptide: Condensin complex subunit 3
    • Protein or peptide: Condensin complex subunit 2
    • DNA: Synthetic DNA ligand
    • DNA: synthetic DNA ligand
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation ...negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation / mitotic sister chromatid segregation / condensed chromosome / cell division / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Condensin complex subunit 2 / Condensin complex subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsLecomte L / Hassler M / Haering C / Eustermann S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)681365European Union
CitationJournal: Science / Year: 2022
Title: A hold-and-feed mechanism drives directional DNA loop extrusion by condensin.
Authors: Indra A Shaltiel / Sumanjit Datta / Léa Lecomte / Markus Hassler / Marc Kschonsak / Sol Bravo / Catherine Stober / Jenny Ormanns / Sebastian Eustermann / Christian H Haering /
Abstract: Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that ...Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop transiently in two separate chambers. Single-molecule imaging and cryo-electron microscopy suggest a putative power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon adenosine triphosphate binding, whereas the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of "motor" and "anchor" chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the SMC reaction cycle determines the directionality of DNA loop extrusion.
History
DepositionDec 6, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 15, 2022-
Current statusJun 15, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13950.png

Downloads & links

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Map

FileDownload / File: emd_13950.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM half map 1 of S.c. condensin peripheral Ycg1 complex bound to DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.029856963 - 2.2384748
Average (Standard dev.)0.0011120869 (±0.025230687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13950_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoEM map of S.c. condensin peripheral Ycg1 complex...

Fileemd_13950_additional_1.map
AnnotationcryoEM map of S.c. condensin peripheral Ycg1 complex bound to DNA local-resolution filtered and postprocessed cryo map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cryoEM map of S.c. condensin peripheral Ycg1...

Fileemd_13950_additional_2.map
Annotationunsharpened cryoEM map of S.c. condensin peripheral Ycg1 complex bound to DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM half map 2 of S.c. condensin peripheral...

Fileemd_13950_half_map_1.map
AnnotationcryoEM half map 2 of S.c. condensin peripheral Ycg1 complex bound to DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM half map 2 of S.c. condensin peripheral...

Fileemd_13950_half_map_2.map
AnnotationcryoEM half map 2 of S.c. condensin peripheral Ycg1 complex bound to DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S.c. Condensin peripheral Ycg1 complex bound to DNA

EntireName: S.c. Condensin peripheral Ycg1 complex bound to DNA
Components
  • Complex: S.c. Condensin peripheral Ycg1 complex bound to DNA
    • Protein or peptide: Condensin complex subunit 3
    • Protein or peptide: Condensin complex subunit 2
    • DNA: Synthetic DNA ligand
    • DNA: synthetic DNA ligand

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Supramolecule #1: S.c. Condensin peripheral Ycg1 complex bound to DNA

SupramoleculeName: S.c. Condensin peripheral Ycg1 complex bound to DNA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 707 KDa

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Macromolecule #1: Condensin complex subunit 3

MacromoleculeName: Condensin complex subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 117.981 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MQDPDGIDIN TKIFNSVAEV FQKAQGSYAG HRKHIAVLKK IQSKAVEQGY EDAFNFWFDK LVTKILPLKK NEIIGDRIVK LVAAFIASL ERELILAKKQ NYKLTNDEEG IFSRFVDQFI RHVLRGVESP DKNVRFRVLQ LLAVIMDNIG EIDESLFNLL I LSLNKRIY ...String:
MQDPDGIDIN TKIFNSVAEV FQKAQGSYAG HRKHIAVLKK IQSKAVEQGY EDAFNFWFDK LVTKILPLKK NEIIGDRIVK LVAAFIASL ERELILAKKQ NYKLTNDEEG IFSRFVDQFI RHVLRGVESP DKNVRFRVLQ LLAVIMDNIG EIDESLFNLL I LSLNKRIY DREPTVRIQA VFCLTKFQDE EQTEHLTELS DNEENFEATR TLVASIQNDP SAEVRRAAML NLINDNNTRP YI LERARDV NIVNRRLVYS RILKSMGRKC FDDIEPHIFD QLIEWGLEDR ELSVRNACKR LIAHDWLNAL DGDLIELLEK LDV SRSSVC VKAIEALFQS RPDILSKIKF PESIWKDFTV EIAFLFRAIY LYCLDNNITE MLEENFPEAS KLSEHLNHYI LLRY HHNDI SNDSQSHFDY NTLEFIIEQL SIAAERYDYS DEVGRRSMLT VVRNMLALTT LSEPLIKIGI RVMKSLSINE KDFVT MAIE IINDIRDDDI EKQEQEEKIK SKKINRRNET SVDEEDENGT HNDEVNEDEE DDNISSFHSA VENLVQGNGN VSESDI INN LPPEKEASSA TIVLCLTRSS YMLELVNTPL TENILIASLM DTLITPAVRN TAPNIRELGV KNLGLCCLLD VKLAIDN MY ILGMCVSKGN ASLKYIALQV IVDIFSVHGN TVVDGEGKVD SISLHKIFYK VLKNNGLPEC QVIAAEGLCK LFLADVFT D DDLFETLVLS YFSPINSSNE ALVQAFAFCI PVYCFSHPAH QQRMSRTAAD ILLRLCVLWD DLQSSVIPEV DREAMLKPN IIFQQLLFWT DPRNLVNQTG STKKDTVQLT FLIDVLKIYA QIEKKEIKKM IITNINAIFL SSEQDYSTLK ELLEYSDDIA ENDNLDNVS KNALDKLRNN LNSLIEEINE RSETQTKDEN NTANDQYSSI LGNSFNKSSN DTIEHAADIT DGNNTELTKT T VNISAVDN TTEQSNSRKR TRSEAEQIDT SKNLENMSIQ DTSTVAKNVS FVLPDEKSDA MSIDEEDKDS ESFSEVC

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Macromolecule #2: Condensin complex subunit 2

MacromoleculeName: Condensin complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 92.721219 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV ...String:
MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV EFETIKMKEL DQELIIDPLF KKALVDFDEG GAKSLLLNTL NIDNTARVIF DASIKDTQNV GQGKLQRKEE EL IERDSLV DDENEPSQSL ISTRNDSTVN DSVISAPSME DEILSLGMDF IKFDQIAVCE ISGSIEQLRN VVEDINQAKD FIE NVNNRF DNFLTEEELQ AAVPDNAEDD SDGFDMGMQQ ELCYPDENHD NTSHDEQDDD NVNSTTGSIF EKDLMAYFDE NLNR NWRGR EHWKVRNFKK ANLVNKESDL LEETRTTIGD TTDKNTTDDK SMDTKKKHKQ KKVLEIDFFK TDDSFEDKVF ASKGR TKID MPIKNRKNDT HYLLPDDFHF STDRITRLFI KPAQKMSLFS HRKHTRGDVS SGLFEKSTVS ANHSNNDIPT IADEHF WAD NYERKEQEEK EKEQSKEVGD VVGGALDNPF EDDMDGVDFN QAFEGTDDNE EASVKLDLQD DEDHKFPIRE NKVTYSR VS KKVDVRRLKK NVWRSINNLI QEHDSRKNRE QSSNDSETHT EDESTKELKF SDIIQGISKM YSDDTLKDIS TSFCFICL L HLANEHGLQI THTENYNDLI VNYEDLATTQ AASLVGGGHH RPHHGGHHHH HHGGRIFYPY DVPDYAGYPY DVPDYAGSY PYDVPNYAAG H

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Macromolecule #3: Synthetic DNA ligand

MacromoleculeName: Synthetic DNA ligand / type: dna / ID: 3
Details: 50bp synthetic DNA ligand with the sequence: 5'-GTTGACAGTG TCGCAACCTG CACAGGCAAG CTGCTGAGTC TGGTGTAGAC-3' The DNA ligand was modelled as poly(dA) as the register could not be determined by cryoEM density.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.615376 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)

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Macromolecule #4: synthetic DNA ligand

MacromoleculeName: synthetic DNA ligand / type: dna / ID: 4
Details: 50bp synthetic DNA ligand with the sequence: 5'-GTCTACACCAGACTCAGCAGCTTGCCTGTGCAGGTTGCGACACTGTCAAC-3' The DNA ligand was modelled as poly(dT) as the register could not be determined by cryoEM density.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.164683 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

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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

Concentration0.707 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium Chloride
20.0 mMHepesHepes
1.0 mMDTTDithiothreitol
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6544 / Average exposure time: 8.0 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 91522
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 27701
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 95000 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5oqn

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7qfw:
S.c. Condensin peripheral Ycg1 subcomplex bound to DNA

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