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- PDB-8rok: Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conforma... -

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Basic information

Entry
Database: PDB / ID: 8rok
TitleHuman cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1
Components
  • Double-strand-break repair protein rad21 homolog
  • Structural maintenance of chromosomes protein 3
KeywordsNUCLEAR PROTEIN / 3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / 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 ...negative regulation of mitotic metaphase/anaphase transition / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / 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 / lateral element / replication-born double-strand break repair via sister chromatid exchange / mediator complex binding / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / lncRNA binding / sister chromatid cohesion / negative regulation of interleukin-1 beta production / microtubule motor activity / stem cell population maintenance / mitotic sister chromatid cohesion / dynein complex binding / mitotic spindle pole / beta-tubulin binding / regulation of DNA replication / 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 / spindle pole / nuclear matrix / Separation of Sister Chromatids / double-strand break repair / mitotic cell cycle / chromosome / midbody / double-stranded DNA binding / 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 / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / 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 ...Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Double-strand-break repair protein rad21 homolog / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Revision 1.2Sep 25, 2024Group: Structure summary / Category: struct / Item: _struct.title

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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 3
B: Double-strand-break repair protein rad21 homolog
C: Structural maintenance of chromosomes protein 3
D: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1148
Polymers130,0194
Non-polymers1,0954
Water1,62190
1
A: Structural maintenance of chromosomes protein 3
B: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,0092
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-48 kcal/mol
Surface area21880 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein 3
D: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,0092
Non-polymers5482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-49 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.244, 154.459, 136.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Structural maintenance of chromosomes protein 3 / SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / ...SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate proteoglycan 6 / Chromosome-associated polypeptide / hCAP


Mass: 52391.367 Da / Num. of mol.: 2 / Mutation: E1144Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC3, BAM, BMH, CSPG6, SMC3L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQE7
#2: Protein Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 12617.939 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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 58135 / % possible obs: 98 % / Redundancy: 13.6 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.32
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.233 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 8944 / CC1/2: 0.816 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.21 Å / SU ML: 0.3738 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 33.5302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 5433 4.84 %
Rwork0.202 106724 -
obs0.2045 58103 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7587 0 0 90 7677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767724
X-RAY DIFFRACTIONf_angle_d0.927410373
X-RAY DIFFRACTIONf_chiral_restr0.05021149
X-RAY DIFFRACTIONf_plane_restr0.00521307
X-RAY DIFFRACTIONf_dihedral_angle_d20.7392950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.57841270.47793017X-RAY DIFFRACTION81.54
2.28-2.30.42562000.38413464X-RAY DIFFRACTION97.58
2.3-2.330.4011630.35743566X-RAY DIFFRACTION98.26
2.33-2.360.41071520.33823604X-RAY DIFFRACTION97.89
2.36-2.390.35222350.3223515X-RAY DIFFRACTION97.96
2.39-2.430.37181960.31413554X-RAY DIFFRACTION97.96
2.43-2.460.37711730.2953524X-RAY DIFFRACTION98.3
2.46-2.50.37771650.28243626X-RAY DIFFRACTION98.26
2.5-2.540.35361700.27643558X-RAY DIFFRACTION98.13
2.54-2.580.36471840.28153617X-RAY DIFFRACTION98.47
2.58-2.620.32281460.26893548X-RAY DIFFRACTION98.27
2.62-2.670.31971610.27283543X-RAY DIFFRACTION98.3
2.67-2.720.32791930.25763580X-RAY DIFFRACTION98.46
2.72-2.780.32941980.24273570X-RAY DIFFRACTION98.33
2.78-2.840.31731830.25643548X-RAY DIFFRACTION98.52
2.84-2.90.33631810.25513576X-RAY DIFFRACTION98.35
2.9-2.980.29171650.23753562X-RAY DIFFRACTION98.65
2.98-3.060.30262050.23223594X-RAY DIFFRACTION99.11
3.06-3.150.27971890.22843572X-RAY DIFFRACTION98.64
3.15-3.250.27662010.2123598X-RAY DIFFRACTION99.29
3.25-3.360.22681770.20823598X-RAY DIFFRACTION98.93
3.36-3.50.25992090.20733553X-RAY DIFFRACTION99.13
3.5-3.660.26171950.20343594X-RAY DIFFRACTION99.11
3.66-3.850.27831980.18973549X-RAY DIFFRACTION98.87
3.85-4.090.19771360.17153647X-RAY DIFFRACTION98.88
4.09-4.410.19912020.15433626X-RAY DIFFRACTION99.58
4.41-4.850.20751810.14283585X-RAY DIFFRACTION99.52
4.85-5.550.20391830.15913600X-RAY DIFFRACTION99.66
5.55-6.990.23761770.18043664X-RAY DIFFRACTION99.74
6.99-47.210.17531880.14863572X-RAY DIFFRACTION99.13
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)
10.6199256435840.1744379695930.1448716653140.9912519136690.4602198599980.007189579822580.109394952128-0.0226580542499-0.04588674738020.0236425199296-0.0892532580574-0.00139702081411-0.145103309650.066282977969-0.0034811372980.3509118077560.02365054716540.05505201006570.33844400879-0.008834981090680.368372044368-35.978243755416.134056910526.7021167635
20.0663496357116-0.0267121953611-0.04146580055680.156546910351-0.06956144646930.06042658501370.1715621171650.261564647682-0.0805613696362-0.573411804181-0.214049780584-0.6196617163940.2473458650240.0338832617270.0004570286887720.6207161150740.04566073870790.1521839180840.529172371877-0.08135506023350.814964822237-47.9793561279-7.0681562929418.878433342
30.516249749412-0.64558314896-0.4112947676091.028678686930.7449236128340.7426102750290.08736510424220.07985118462810.00844991821311-0.144262214495-0.0983763118078-0.0908749649294-0.00434630899765-0.143781797531.4391144233E-50.425667839182-0.0520252077068-0.01776401589540.3951842252980.009607513348260.353287069597-37.574922122354.874576960147.8579910352
40.1724792047660.08460452835840.1277507436480.31323819534-0.0747867515160.1580629539610.297213674104-0.009675381108470.0348358785376-0.0608951852373-0.15398764508-0.318331898121-0.352057259693-0.2875085935630.0001084032600190.508686980810.0325979524642-0.06141080263590.537689160883-0.007948040923820.522462103723-49.677846478476.619664815155.0010242665
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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