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- PDB-8pq5: Human Cohesin ATPase module with an open DNA exit gate -

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Basic information

Entry
Database: PDB / ID: 8pq5
TitleHuman Cohesin ATPase module with an open DNA exit gate
Components
  • 64-kDa C-terminal product
  • Structural maintenance of chromosomes protein 1A
  • Structural maintenance of chromosomes protein 3
KeywordsDNA BINDING PROTEIN / 3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle / Cell cycle / DNA binding
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process ...negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / chromosome segregation / nuclear matrix / spindle pole / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / 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 / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Double-strand-break repair protein rad21 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLandwerlin, P. / Durand, A. / Diebold-Durand, M.-L. / Romier, C.
Funding support France, 7items
OrganizationGrant numberCountry
Fondation ARCARCPJA20181208268 France
Fondation ARCARCPJA2021060003715 France
Fondation ARCDOC20180507150 France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-01 France
CitationJournal: Cell Rep / Year: 2024
Title: The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains.
Authors: Marina Vitoria Gomes / Pauline Landwerlin / Marie-Laure Diebold-Durand / Tajith B Shaik / Alexandre Durand / Edouard Troesch / Chantal Weber / Karl Brillet / Marianne Victoria Lemée / ...Authors: Marina Vitoria Gomes / Pauline Landwerlin / Marie-Laure Diebold-Durand / Tajith B Shaik / Alexandre Durand / Edouard Troesch / Chantal Weber / Karl Brillet / Marianne Victoria Lemée / Christophe Decroos / Ludivine Dulac / Pierre Antony / Erwan Watrin / Eric Ennifar / Christelle Golzio / Christophe Romier /
Abstract: Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we ...Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.
History
DepositionJul 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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 1A
B: Structural maintenance of chromosomes protein 3
C: 64-kDa C-terminal product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0535
Polymers113,0383
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Structural maintenance of chromosomes protein 1A


Mass: 51443.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC1A, DXS423E, KIAA0178, SB1.8, SMC1, SMC1L1 / Production host: Escherichia coli (E. coli)
#2: Protein Structural maintenance of chromosomes protein 3


Mass: 52391.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Smc3, Bam, Bmh, Cspg6, Mmip1, Smc3l1, Smcd / Production host: Escherichia coli (E. coli)
#3: Protein 64-kDa C-terminal product / 64-kDa carboxy-terminal product / 65-kDa carboxy-terminal product


Mass: 9203.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1, SCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60216
#4: 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
Has ligand of interestY
Has protein modificationN

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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: Human Cohesin ATP-open-engaged ATPase module / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solution
IDSpecimen-IDpH
118.2
228.2
338.2
Specimen
IDExperiment-IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
11NONONOYES
21NONONOYES
31NONONOYES
Specimen support
IDSpecimen-IDGrid materialGrid mesh size (divisions/in.)Grid type
11GOLD300C-flat-1.2/1.3
22COPPER300C-flat-1.2/1.3
33GOLDC-flat-1.2/1.3
Vitrification
IDInstrumentCryogen nameSpecimen-IDEntry-ID
1FEI VITROBOT MARK IVETHANE18PQ5
2FEI VITROBOT MARK IVETHANE28PQ5
3FEI VITROBOT MARK IVETHANE38PQ5

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Electron microscopy imaging

EM imaging

Accelerating voltage: 200 kV / Alignment procedure: COMA FREE / C2 aperture diameter: 30 µm / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS GLACIOS / Mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 800 nm / Nominal magnification: 45000 X / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

IDNominal defocus max (nm)Specimen-ID
120001
230002
320003
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector modelNum. of grids imagedNum. of real images
1144.4COUNTINGGATAN K2 SUMMIT (4k x 4k)14146
2263.85COUNTINGGATAN K2 SUMMIT (4k x 4k)15574
3343.61COUNTINGGATAN K2 SUMMIT (4k x 4k)11593

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Processing

EM software
IDNameCategory
1Warpparticle selection
4WarpCTF correction
7PHENIXmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14RELION3D reconstruction
15PHENIXmodel refinement
Image processingDetails: All three data sets processed together.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7098916
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144721 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8P0A

8p0a


Accession code: 8P0A / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036409
ELECTRON MICROSCOPYf_angle_d0.6648622
ELECTRON MICROSCOPYf_dihedral_angle_d6.404850
ELECTRON MICROSCOPYf_chiral_restr0.047946
ELECTRON MICROSCOPYf_plane_restr0.0051108

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