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- PDB-7q2x: Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (... -

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Basic information

Entry
Database: PDB / ID: 7q2x
TitleCryo-EM structure of clamped S.cerevisiae condensin-DNA complex (Form I)
Components
  • (Condensin complex subunit ...) x 2
  • (DNA (36-MER)) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
KeywordsCELL CYCLE / condensin / SMC
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 / synaptonemal complex assembly ...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 / 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
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'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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 S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLee, B.-G. / Rhodes, J. / Lowe, J.
Funding support United Kingdom, 3items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 13, 2022Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 2
B: Structural maintenance of chromosomes protein 4
C: Condensin complex subunit 2
D: Condensin complex subunit 1
F: DNA (36-MER)
G: DNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,17312
Polymers538,1386
Non-polymers1,0356
Water0
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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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB

#1: Protein Structural maintenance of chromosomes protein 2 / DA-box protein SMC2 / Smc2


Mass: 134125.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SMC2, YFR031C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): W303-1a / References: UniProt: P38989
#2: Protein Structural maintenance of chromosomes protein 4 / Smc4


Mass: 162435.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: comment: since alignment with full sequence did not work, we input only sequence in pdb. The real sequence is UNIPROT Q12267 (full-length construct),comment: since alignment with full ...Details: comment: since alignment with full sequence did not work, we input only sequence in pdb. The real sequence is UNIPROT Q12267 (full-length construct),comment: since alignment with full sequence did not work, we input only sequence in pdb. The real sequence is UNIPROT Q12267 (full-length construct)
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SMC4, YLR086W, L9449.5 / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12267

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

#3: Protein Condensin complex subunit 2 / / Barren homolog / CAPH homolog / Brn1


Mass: 86323.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: BRN1, YBL097W, YBL0830 / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P38170
#4: Protein Condensin complex subunit 1 / / XCAP-D2 homolog / Ycs4


Mass: 133116.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: YCS4, LOC7, YLR272C, L8479.14 / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q06156

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DNA chain , 2 types, 2 molecules FG

#5: DNA chain DNA (36-MER)


Mass: 11230.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (36-MER)


Mass: 10905.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 6 molecules

#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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: complex of condensin tetramer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 515 kDa/nm / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae W303 (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELIONparticle selection
3EPUimage acquisition
6CTFFIND4CTF correction
9UCSF Chimeramodel fitting
10Cootmodel fitting
12RELIONinitial Euler assignment
13RELIONfinal Euler assignment
15RELION3D reconstruction
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286294 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
16YVU

6yvu

A1
26YVU

6yvu

B1
36YVU

6yvu

C1
46YVU

6yvu

D1
56ZZ6

6zz6

E1
66ZZ6

6zz6

F1

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