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- PDB-8roh: Human cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformation -

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Basic information

Entry
Database: PDB / ID: 8roh
TitleHuman cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformation
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 / 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 / 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 / microtubule motor activity / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / stem cell population maintenance / lncRNA binding / mitotic spindle pole / dynein complex binding / 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 / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / nuclear matrix / spindle pole / 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 / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / membrane / 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
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: 2.6 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 1.2Sep 25, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 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 3
B: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4476
Polymers67,0672
Non-polymers3804
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-83 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.789, 90.789, 236.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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: 54448.754 Da / Num. of mol.: 1 / 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.: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.21M NaSO4 ; 0.1M Bis-tris propane pH 7; 16% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31414 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 60.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.28 / Net I/σ(I): 14.93
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 25.7 % / Rmerge(I) obs: 3.842 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 4948 / CC1/2: 0.366 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.6 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 0.48 / Phase error: 30.9996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 2760 4.75 %
Rwork0.2164 55400 -
obs0.2183 31408 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 21 9 4081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824136
X-RAY DIFFRACTIONf_angle_d0.89875543
X-RAY DIFFRACTIONf_chiral_restr0.0499612
X-RAY DIFFRACTIONf_plane_restr0.0079702
X-RAY DIFFRACTIONf_dihedral_angle_d17.05721583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.39091240.36732722X-RAY DIFFRACTION98.61
2.64-2.690.38161260.3642781X-RAY DIFFRACTION99.97
2.69-2.740.39181290.34742792X-RAY DIFFRACTION100
2.74-2.80.37341500.3372742X-RAY DIFFRACTION100
2.8-2.860.35281360.34762802X-RAY DIFFRACTION99.97
2.86-2.930.35721470.352766X-RAY DIFFRACTION99.97
2.93-30.32521310.30682758X-RAY DIFFRACTION99.97
3-3.080.37971150.30462799X-RAY DIFFRACTION100
3.08-3.170.35591400.28272778X-RAY DIFFRACTION100
3.17-3.270.31241510.26662741X-RAY DIFFRACTION100
3.27-3.390.28811530.24962787X-RAY DIFFRACTION100
3.39-3.530.27621490.24612736X-RAY DIFFRACTION100
3.53-3.690.29981670.19682760X-RAY DIFFRACTION100
3.69-3.880.24031510.17982768X-RAY DIFFRACTION99.97
3.88-4.120.22441420.17812775X-RAY DIFFRACTION100
4.12-4.440.2032980.17042797X-RAY DIFFRACTION100
4.44-4.890.17461370.1592771X-RAY DIFFRACTION99.97
4.89-5.60.24261230.17412804X-RAY DIFFRACTION100
5.6-7.050.24331540.22062754X-RAY DIFFRACTION99.97
7.05-49.60.17361370.16332767X-RAY DIFFRACTION99.66
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)
10.230098777155-0.0536346173830.3590708930370.36737223843-0.2718935457021.98008926545-0.05691029293880.1826459077410.007274210037680.09603044846670.008983252783450.0125988332533-0.347312672737-0.1467913444738.56947406238E-70.3697829107220.00950610664928-0.02936608599250.5550670850910.006149133413750.510958289941-34.1897844747-12.8973032515-19.7550591654
20.353313267083-0.1805767653830.3040867705280.117470818035-0.1159237323190.296971715406-0.07060411344930.122017650649-0.174402532959-0.061787742387-0.0355785134446-0.0685986480146-0.0524204923893-0.0907344055102-4.38978337271E-50.627581769824-0.055716849135-0.04192644141480.505502418607-0.03556085981580.572117059984-31.6919032119-12.07951528713.07875206598
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - E1 - 21001
22chain BBF4 - 901 - 87

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