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- PDB-7qen: S.c. Condensin core in DNA- and ATP-bound state -

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Basic information

Entry
Database: PDB / ID: 7qen
TitleS.c. Condensin core in DNA- and ATP-bound state
Components
  • (Condensin complex subunit ...) x 2
  • (DNA (35-MER)) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
KeywordsDNA BINDING PROTEIN / SMC-motor protein
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 / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy ...negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / 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 / histone binding / double-stranded DNA 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 / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / 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 / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / 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
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / 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 CEN.PK113-7D (yeast)
Saccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLecomte, L. / Hassler, M. / Haering, C. / Eustermann, S.
Funding supportEuropean Union, 1items
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 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: DNA (35-MER)
G: DNA (35-MER)
B: Structural maintenance of chromosomes protein 4
A: Structural maintenance of chromosomes protein 2
C: Condensin complex subunit 2
D: Condensin complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)559,52210
Polymers558,4596
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules FG

#1: DNA chain DNA (35-MER)


Mass: 15615.376 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 50-mer DNA ligand (sequence below) was modelled as poly-dA due to missing sequence register 5'-GTTGACAGTG TCGCAACCTG CACAGGCAAG CTGCTGAGTC TGGTGTAGAC-3'
Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (35-MER)


Mass: 15164.683 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 50-mer DNA ligand (sequence below) was modelled as poly-dT due to missing sequence register. 5'-GTCTACACCAGACTCAGCAGCTTGCCTGTGCAGGTTGCGACACTGTCAAC-3'
Source: (synth.) synthetic construct (others)

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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules BA

#3: Protein Structural maintenance of chromosomes protein 4


Mass: 167716.125 Da / Num. of mol.: 1 / Mutation: E1352Q
Source method: isolated from a genetically manipulated source
Details: ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to ...Details: ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.,ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.,ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.
Source: (gene. exp.) Saccharomyces cerevisiae CEN.PK113-7D (yeast), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMC4, YLR086W, L9449.5 / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12267
#4: Protein Structural maintenance of chromosomes protein 2 / DA-box protein SMC2


Mass: 134124.891 Da / Num. of mol.: 1 / Mutation: E1114Q
Source method: isolated from a genetically manipulated source
Details: ATPase deficient Walker B motif mutant
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMC2, YFR031C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38989

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Condensin complex subunit ... , 2 types, 2 molecules CD

#5: Protein Condensin complex subunit 2 / Barren homolog / CAPH homolog


Mass: 92721.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: BRN1, YBL097W, YBL0830 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38170
#6: Protein Condensin complex subunit 1 / XCAP-D2 homolog


Mass: 133116.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YCS4, LOC7, YLR272C, L8479.14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06156

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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: ATP- and DNA- bound Sc Condensin core complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 645 kDa/nm / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium ChlorideNaCl1
220 mMHepesHepes1
31 mMDithiothreitolDTT1
45 mMMagnesium ChlorideMgCl21
SpecimenConc.: 0.645 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 2 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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 / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / 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: 8 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6544
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11RELION3.1.3initial Euler assignment
12RELION3.1.3final Euler assignment
13RELION3.1.3classification
14RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 91522
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66205 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6YVU

6yvu


Accession code: 6YVU / Source name: PDB / Type: experimental model

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