+Open data
-Basic information
Entry | Database: PDB / ID: 7qen | ||||||
---|---|---|---|---|---|---|---|
Title | S.c. Condensin core in DNA- and ATP-bound state | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / SMC-motor protein | ||||||
Function / homology | Function and homology information negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly / nucleophagy / 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 | ||||||
Biological species | Saccharomyces cerevisiae CEN.PK113-7D (yeast) Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | ||||||
Authors | Lecomte, L. / Hassler, M. / Haering, C. / Eustermann, S. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qen.cif.gz | 484.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qen.ent.gz | 355.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qen_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qen_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7qen_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 7qen_validation.cif.gz | 108.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/7qen ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qen | HTTPS FTP |
-Related structure data
Related structure data | 13934MC 7qfwC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA chain , 2 types, 2 molecules FG
#1: DNA chain | 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 | 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) |
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules BA
#3: Protein | 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 | 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 |
-Condensin complex subunit ... , 2 types, 2 molecules CD
#5: Protein | 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 | 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 |
-Non-polymers , 2 types, 4 molecules
#7: Chemical | #8: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ATP- and DNA- bound Sc Condensin core complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 645 kDa/nm / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 0.645 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 2 divisions/in. / Grid type: Quantifoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 optics | Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 91522 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66205 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6YVU Accession code: 6YVU / Source name: PDB / Type: experimental model |