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- PDB-6qpw: Structural basis of cohesin ring opening -

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Basic information

Entry
Database: PDB / ID: 6qpw
TitleStructural basis of cohesin ring opening
Components
  • (Sister chromatid cohesion protein ...) x 2
  • (Structural maintenance of chromosomes ...) x 2
KeywordsCELL CYCLE / Chromatin / genome segregation / cohesin
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / double-strand break repair / double-stranded DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein ...Structural maintenance of chromosome 1. Chain E / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Structural maintenance of chromosomes protein / Structural maintenance of chromosomes protein 3 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPanne, D. / Muir, K.W. / Li, Y. / Weis, F.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening.
Authors: Kyle W Muir / Yan Li / Felix Weis / Daniel Panne /
Abstract: Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring- ...Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
History
DepositionFeb 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Feb 5, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _em_admin.last_update / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id
Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
B: Sister chromatid cohesion protein 1
C: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
E: Sister chromatid cohesion protein 1,Structural maintenance of chromosomes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4998
Polymers140,4044
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14430 Å2
ΔGint-103 kcal/mol
Surface area39520 Å2
MethodPISA

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Components

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Structural maintenance of chromosomes ... , 2 types, 2 molecules AC

#1: Protein Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein


Mass: 27570.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0066330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SGH3
#3: Protein Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3 / DA-box protein SMC3


Mass: 61051.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SMC3, YJL074C, J1049 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47037

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Sister chromatid cohesion protein ... , 2 types, 2 molecules BE

#2: Protein Sister chromatid cohesion protein 1


Mass: 9489.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12158
#4: Protein Sister chromatid cohesion protein 1,Structural maintenance of chromosomes protein


Mass: 42292.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04, CTHT_0066330
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12158, UniProt: G0SGH3

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Cohesin ATPase head moduleCOMPLEX#1-#40MULTIPLE SOURCES
2Structural maintenance of chromosomes protein,Structural maintenance of chromosomes proteinCOMPLEX#11RECOMBINANT
3Sister chromatid cohesion protein 1, Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3COMPLEX#2-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)759272
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
23Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD
Image recordingElectron dose: 42.08 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.13model fitting
12RELION2.1b3D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178162 / Symmetry type: POINT

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