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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 / 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
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: 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
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

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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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