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- PDB-8rof: Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound... -

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Basic information

Entry
Database: PDB / ID: 8rof
TitleHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound 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 / positive regulation of sister chromatid cohesion / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / 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 / positive regulation of sister chromatid cohesion / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / 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 / mediator complex binding / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic sister chromatid cohesion / mitotic spindle pole / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / 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 / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / 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
ADENOSINE-5'-DIPHOSPHATE / 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: 1.65 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: Vitoria Gomes, M. / Landwerlin, P. / Diebold-Durand, M.L. / Shaik, T.B. / Durand, A. / Troesch, E. / Weber, C. / Brillet, K. / Lemee, M.V. / Decroos, C. / Dulac, L. / Antony, P. / Watrin, E. ...Authors: Vitoria Gomes, M. / Landwerlin, P. / Diebold-Durand, M.L. / Shaik, T.B. / Durand, A. / Troesch, E. / Weber, C. / Brillet, K. / Lemee, M.V. / Decroos, C. / Dulac, L. / Antony, P. / Watrin, E. / Ennifar, E. / Golzio, C. / Romier, C.
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3204
Polymers49,8692
Non-polymers4522
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-30 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.453, 113.906, 133.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-2286-

HOH

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Components

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


Mass: 40665.125 Da / Num. of mol.: 1 / 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.: 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride; 0.1 M MES pH 6.0; 20 % 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: 0.999997 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999997 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 61059 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.52
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 13.2 % / Rmerge(I) obs: 2.391 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 9690 / CC1/2: 0.42 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.57 Å / SU ML: 0.2282 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 24.8558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 6024 5.12 %
Rwork0.1955 111543 -
obs0.1972 61052 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 302 3671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673505
X-RAY DIFFRACTIONf_angle_d0.82954748
X-RAY DIFFRACTIONf_chiral_restr0.0552524
X-RAY DIFFRACTIONf_plane_restr0.0054618
X-RAY DIFFRACTIONf_dihedral_angle_d20.7471340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.35772070.34643604X-RAY DIFFRACTION97.92
1.67-1.690.3491710.33743723X-RAY DIFFRACTION99.79
1.69-1.710.38561790.33623747X-RAY DIFFRACTION99.07
1.71-1.730.32742160.33043690X-RAY DIFFRACTION99.92
1.73-1.750.3531830.31993702X-RAY DIFFRACTION99.21
1.75-1.780.33132160.30383737X-RAY DIFFRACTION100
1.78-1.80.32731980.29053723X-RAY DIFFRACTION99.39
1.8-1.830.30041870.27493713X-RAY DIFFRACTION100
1.83-1.860.27552160.27063680X-RAY DIFFRACTION99.59
1.86-1.890.29181760.26343748X-RAY DIFFRACTION99.95
1.89-1.920.29142100.26743724X-RAY DIFFRACTION99.72
1.92-1.960.29812100.26763775X-RAY DIFFRACTION99.8
1.96-20.28982030.22113665X-RAY DIFFRACTION100
2-2.040.21622390.22043677X-RAY DIFFRACTION99.95
2.04-2.080.26012140.21963720X-RAY DIFFRACTION99.95
2.08-2.130.27581690.21343746X-RAY DIFFRACTION100
2.13-2.180.25842150.20383736X-RAY DIFFRACTION100
2.18-2.240.21062290.20663704X-RAY DIFFRACTION100
2.24-2.310.22672030.19533703X-RAY DIFFRACTION99.97
2.31-2.380.22272020.18943725X-RAY DIFFRACTION100
2.38-2.470.22452040.19163745X-RAY DIFFRACTION100
2.47-2.570.26671930.1923709X-RAY DIFFRACTION100
2.57-2.680.24371830.18643760X-RAY DIFFRACTION100
2.68-2.820.2511870.18413732X-RAY DIFFRACTION100
2.82-30.21431800.18593757X-RAY DIFFRACTION100
3-3.230.22312230.183689X-RAY DIFFRACTION100
3.23-3.560.15021730.16583763X-RAY DIFFRACTION100
3.56-4.070.19132020.16063741X-RAY DIFFRACTION100
4.07-5.130.20912180.14783712X-RAY DIFFRACTION100
5.13-43.570.1862180.17593693X-RAY DIFFRACTION99.34
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)
11.11177560853-0.7629088327570.2035788497140.7174261468630.0519385907499-0.1608580062050.0181711302499-0.05307034078660.105274886821-0.075369902341-0.0472017534149-0.00196585276318-0.0105053575579-0.0531101956838-0.01377159716090.1516487020970.02954414633750.02286466685080.1568364203250.001353109841540.12549525885720.025893706541.29218597420.464150363
20.1318507689-0.0636665738838-0.08148553243720.149624245808-0.07908498149850.1245427819390.04672005183680.116419801451-0.17960312940.00116964578433-0.0674557444649-0.1064597249610.1239405711720.0132522779945-0.001733403134480.2238782527770.0203901050018-0.008750556493290.156350822550.00744387640050.24528271314836.714892206810.902262011115.3154900371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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