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- PDB-8ro9: Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P... -

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Basic information

Entry
Database: PDB / ID: 8ro9
TitleHuman cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation
Components
  • 64-kDa C-terminal product
  • Structural maintenance of chromosomes protein 1A
KeywordsNUCLEAR PROTEIN / 3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle
Function / homology
Function and homology information


response to DNA damage checkpoint signaling / 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 ...response to DNA damage checkpoint signaling / 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 / mediator complex binding / 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 / mitotic sister chromatid cohesion / lncRNA binding / mitotic spindle pole / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / response to radiation / kinetochore / spindle pole / nuclear matrix / 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 / protein heterodimerization activity / cell division / DNA repair / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
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 ...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 / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Structural maintenance of chromosomes protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.767 Å
AuthorsVitoria Gomes, M. / 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 / Item: _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: 64-kDa C-terminal product
C: Structural maintenance of chromosomes protein 1A
D: 64-kDa C-terminal product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5765
Polymers121,2944
Non-polymers2821
Water7,008389
1
A: Structural maintenance of chromosomes protein 1A
B: 64-kDa C-terminal product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9293
Polymers60,6472
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-13 kcal/mol
Surface area20380 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein 1A
D: 64-kDa C-terminal product


Theoretical massNumber of molelcules
Total (without water)60,6472
Polymers60,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.918, 64.597, 89.949
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Structural maintenance of chromosomes protein 1A / SMC protein 1A / SMC-1-alpha / SMC-1A / Sb1.8


Mass: 51443.246 Da / Num. of mol.: 2 / Mutation: E1157Q
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) / References: UniProt: Q14683
#2: Protein 64-kDa C-terminal product / 64-kDa carboxy-terminal product / 65-kDa carboxy-terminal product


Mass: 9203.648 Da / Num. of mol.: 2
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: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium bromide; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97995 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97995 Å / Relative weight: 1
ReflectionResolution: 1.767→50 Å / Num. obs: 103953 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.94
Reflection shellResolution: 1.767→1.87 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.277 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 16610 / CC1/2: 0.58 / % possible all: 98.7

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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: 1.767→44.6457 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 10071 4.95 %
Rwork0.1897 --
obs0.1911 103953 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.767→44.6457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 19 389 6787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076619
X-RAY DIFFRACTIONf_angle_d0.8868930
X-RAY DIFFRACTIONf_dihedral_angle_d15.8344067
X-RAY DIFFRACTIONf_chiral_restr0.059978
X-RAY DIFFRACTIONf_plane_restr0.0061167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7673-1.78730.36343200.34776073X-RAY DIFFRACTION93
1.7873-1.80840.353650.33276418X-RAY DIFFRACTION100
1.8084-1.83040.33233430.32196413X-RAY DIFFRACTION100
1.8304-1.85360.32483400.30946495X-RAY DIFFRACTION100
1.8536-1.8780.31853320.29256524X-RAY DIFFRACTION100
1.878-1.90370.32333410.28576412X-RAY DIFFRACTION100
1.9037-1.93090.32823530.27086416X-RAY DIFFRACTION100
1.9309-1.95970.27183620.25226506X-RAY DIFFRACTION100
1.9597-1.99040.25533470.24276412X-RAY DIFFRACTION100
1.9904-2.0230.27112920.2266522X-RAY DIFFRACTION100
2.023-2.05790.22693080.22826458X-RAY DIFFRACTION100
2.0579-2.09530.24953830.22746479X-RAY DIFFRACTION100
2.0953-2.13560.24272920.22046478X-RAY DIFFRACTION100
2.1356-2.17920.2222850.20976530X-RAY DIFFRACTION100
2.1792-2.22660.23173660.1996447X-RAY DIFFRACTION100
2.2266-2.27840.22843450.20166454X-RAY DIFFRACTION100
2.2784-2.33530.25863120.20036417X-RAY DIFFRACTION100
2.3353-2.39850.22743770.19896489X-RAY DIFFRACTION100
2.3985-2.4690.22752880.20266480X-RAY DIFFRACTION100
2.469-2.54870.24763220.20256548X-RAY DIFFRACTION100
2.5487-2.63980.23023510.19466414X-RAY DIFFRACTION100
2.6398-2.74550.25083220.20526487X-RAY DIFFRACTION100
2.7455-2.87040.22063540.20486412X-RAY DIFFRACTION100
2.8704-3.02170.23883420.20226491X-RAY DIFFRACTION100
3.0217-3.2110.22363560.20236498X-RAY DIFFRACTION100
3.211-3.45880.22183150.19026464X-RAY DIFFRACTION100
3.4588-3.80670.18693720.16536412X-RAY DIFFRACTION100
3.8067-4.35720.18063230.14896468X-RAY DIFFRACTION100
4.3572-5.4880.17633480.14456424X-RAY DIFFRACTION100
5.488-44.64570.20343150.17926443X-RAY DIFFRACTION99
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)
10.87820.0403-0.35770.27660.39950.5480.019-0.0234-0.20040.01810.0381-0.0583-0.03830.08410.00640.27580.003-0.01690.26250.02360.3137-40.019314.656719.964
20.1464-0.0331-0.0140.14710.01280.10340.0625-0.3940.07170.2247-0.03410.0668-0.2897-0.18990.00010.3908-0.00580.03210.37470.00120.2716-56.383132.368444.6774
31.01590.15580.20770.54890.25250.67690.08520.07-0.12680.0318-0.0212-0.08740.04760.170600.28160.003-0.00480.30230.02290.3085-31.842116.634367.2638
40.0679-0.04660.05140.18520.08160.2750.1015-0.1510.06650.2382-0.02640.0176-0.1998-0.11120.00010.4443-0.0670.01040.34330.01340.2833-42.981332.213390.837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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