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- PDB-8ro6: Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loo... -

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Basic information

Entry
Database: PDB / ID: 8ro6
TitleHuman cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformation
Components
  • 64-kDa C-terminal product
  • Structural maintenance of chromosomes protein 1A (SMC1A)
KeywordsNUCLEAR PROTEIN / 3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle
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
Double-strand-break repair protein rad21 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShaik, T.B. / 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
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 1A (SMC1A)
B: 64-kDa C-terminal product


Theoretical massNumber of molelcules
Total (without water)60,6482
Polymers60,6482
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.930, 64.720, 47.340
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Structural maintenance of chromosomes protein 1A (SMC1A)


Mass: 51444.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.0; 10% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.07505 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07505 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27871 / % possible obs: 96.2 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.08
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.196 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 3967 / CC1/2: 0.513 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.1247 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1394 5 %
Rwork0.1899 --
obs0.1925 27871 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.1247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 0 79 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083310
X-RAY DIFFRACTIONf_angle_d0.9134458
X-RAY DIFFRACTIONf_dihedral_angle_d14.4052036
X-RAY DIFFRACTIONf_chiral_restr0.057489
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27870.40471330.38392506X-RAY DIFFRACTION93
2.2787-2.36990.34671350.27582572X-RAY DIFFRACTION96
2.3699-2.47770.29861360.22472581X-RAY DIFFRACTION97
2.4777-2.60840.26841390.21922642X-RAY DIFFRACTION99
2.6084-2.77180.271400.2162667X-RAY DIFFRACTION100
2.7718-2.98570.29181410.22032664X-RAY DIFFRACTION100
2.9857-3.28610.28721400.21922674X-RAY DIFFRACTION100
3.2861-3.76140.2621420.19272692X-RAY DIFFRACTION100
3.7614-4.73830.19371440.15412728X-RAY DIFFRACTION100
4.7383-46.12470.21341440.16622751X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70210.82370.27741.76750.38920.71820.10910.0089-0.05050.173-0.1771-0.32420.03550.1995-00.3311-0.0022-0.03370.40430.08780.405260.272718.805824.1171
20.26590.13480.06180.26230.19410.1740.06760.3106-0.3603-0.7098-0.11340.13490.61730.19550.00060.78060.07470.01140.4362-0.05050.373246.14722.0638-0.2936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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