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- PDB-6qnx: Structure of the SA2/SCC1/CTCF complex -

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Basic information

Entry
Database: PDB / ID: 6qnx
TitleStructure of the SA2/SCC1/CTCF complex
Components
  • Cohesin subunit SA-2
  • Double-strand-break repair protein rad21 homolog
  • Transcriptional repressor CTCF
KeywordsGENE REGULATION / Cohesin / CTCF / TAD / Chromatin folding / genome regulation / SA2
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / chromatin insulator sequence binding / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle ...negative regulation of mitotic metaphase/anaphase transition / chromatin insulator sequence binding / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / regulation of centromeric sister chromatid cohesion / negative regulation of glial cell apoptotic process / genomic imprinting / replication-born double-strand break repair via sister chromatid exchange / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic spindle pole / 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 / epigenetic regulation of gene expression / condensed chromosome / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / male germ cell nucleus / chromosome segregation / transcription coregulator binding / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / spindle pole / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA recombination / DNA-binding transcription factor binding / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / sequence-specific DNA binding / transcription cis-regulatory region binding / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / cell division / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / 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 / Stromalin conservative domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA ...: / 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 / Stromalin conservative domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative (SCD) domain profile. / ScpA-like, C-terminal / C2H2-type zinc-finger domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Transcriptional repressor CTCF / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, Y. / Muir, K.W. / Panne, D.
CitationJournal: Nature / Year: 2020
Title: The structural basis for cohesin-CTCF-anchored loops.
Authors: Li, Y. / Haarhuis, J.H.I. / Sedeno Cacciatore, A. / Oldenkamp, R. / van Ruiten, M.S. / Willems, L. / Teunissen, H. / Muir, K.W. / de Wit, E. / Rowland, B.D. / Panne, D.
History
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
SupersessionApr 29, 2020ID: 6QNY
Revision 1.2Apr 29, 2020Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cohesin subunit SA-2
B: Double-strand-break repair protein rad21 homolog
C: Transcriptional repressor CTCF


Theoretical massNumber of molelcules
Total (without water)296,2033
Polymers296,2033
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-40 kcal/mol
Surface area48680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.029, 107.255, 176.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cohesin subunit SA-2 / / SCC3 homolog 2 / Stromal antigen 2


Mass: 141502.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAG2, SA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3U4
#2: Protein Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 71772.352 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: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 82928.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49711
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→45.8 Å / Num. obs: 41804 / % possible obs: 99.6 % / Redundancy: 4.4 % / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.76 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.8 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs41803 99.6 %
Refinement stepCycle: LAST / Resolution: 2.7→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8223 0 0 6 8229

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