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- PDB-9ep3: Structure of the SA2/SCC1/WAPL complex -

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Basic information

Entry
Database: PDB / ID: 9ep3
TitleStructure of the SA2/SCC1/WAPL complex
Components
  • Cohesin subunit SA-2
  • Double-strand-break repair protein rad21 homolog
  • Wings apart-like protein homolog
KeywordsGENE REGULATION / Cohesin / Complex / HEAT Repeat / DNA binding / chromatin binding
Function / homology
Function and homology information


negative regulation of chromatin binding / ATP-dependent protein-DNA unloader activity / negative regulation of sister chromatid cohesion / 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 / mitotic cohesin complex ...negative regulation of chromatin binding / ATP-dependent protein-DNA unloader activity / negative regulation of sister chromatid cohesion / 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 / mitotic cohesin complex / positive regulation of sister chromatid cohesion / negative regulation of glial cell apoptotic process / negative regulation of G2/M transition of mitotic cell cycle / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic spindle pole / lncRNA binding / negative regulation of DNA replication / mitotic sister chromatid segregation / 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 / intercellular bridge / 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 / fibrillar center / Separation of Sister Chromatids / spindle pole / mitotic spindle / double-strand break repair / chromosome / midbody / DNA recombination / DNA-binding transcription factor binding / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / intracellular membrane-bounded organelle / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
WAPL domain / Wings apart-like protein, C-terminal / Wings apart-like protein / Wings apart-like protein regulation of heterochromatin / WAPL domain profile. / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA ...WAPL domain / Wings apart-like protein, C-terminal / Wings apart-like protein / Wings apart-like protein regulation of heterochromatin / WAPL domain profile. / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / 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 / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Wings apart-like protein homolog / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsGraham, J.J. / Panne, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust221881/Z/20/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W001667/1 United Kingdom
CitationJournal: To Be Published
Title: Structural basis for cohesin release and control of genome looping by WAPL
Authors: Graham, J.J. / Panne, D.
History
DepositionMar 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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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: Wings apart-like protein homolog


Theoretical massNumber of molelcules
Total (without water)132,3023
Polymers132,3023
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-44 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.433, 107.440, 181.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 113610.039 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 / 64-kDa carboxy-terminal product / 65-kDa carboxy-terminal product


Mass: 16049.612 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/peptide Wings apart-like protein homolog / Friend of EBNA2 protein / WAPL cohesin release factor


Mass: 2641.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z5K2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 291 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: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 3.08→47.97 Å / Num. obs: 28667 / % possible obs: 98.6 % / Redundancy: 4.4 % / CC1/2: 0.99 / Net I/σ(I): 9.2
Reflection shellResolution: 3.08→3.26 Å / Num. unique obs: 2797 / CC1/2: 0.375 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→47.97 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 1391 4.85 %
Rwork0.2244 --
obs0.2265 28667 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8314 0 0 60 8374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038473
X-RAY DIFFRACTIONf_angle_d0.52211427
X-RAY DIFFRACTIONf_dihedral_angle_d4.3361104
X-RAY DIFFRACTIONf_chiral_restr0.0331295
X-RAY DIFFRACTIONf_plane_restr0.0031447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.190.41841290.39382594X-RAY DIFFRACTION95
3.19-3.310.36721330.31972726X-RAY DIFFRACTION99
3.31-3.460.27391310.28512707X-RAY DIFFRACTION98
3.46-3.650.39291370.28052705X-RAY DIFFRACTION99
3.65-3.870.26361470.22042728X-RAY DIFFRACTION99
3.88-4.170.25541290.21052746X-RAY DIFFRACTION99
4.17-4.590.25361320.19642766X-RAY DIFFRACTION99
4.59-5.260.22731700.20212709X-RAY DIFFRACTION98
5.26-6.620.30161520.24932794X-RAY DIFFRACTION99
6.62-47.970.23321310.19092801X-RAY DIFFRACTION94
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)
14.22541.46673.28732.61580.25226.60420.42480.2632-0.5601-0.0950.1831-0.5280.00080.71870.60921.332-0.059-0.36371.3556-0.46880.589-45.2292-40.9287-23.4529
25.67841.1388-2.4233.8036-1.06013.3211-0.51571.0336-1.1238-0.53530.0979-0.66690.6274-0.05640.15370.7494-0.0414-0.03510.6511-0.06990.705-42.8883-42.4471-13.1391
32.16760.5772-1.40041.66190.67152.1460.4559-0.3341-0.74550.3828-0.4850.539-0.3337-0.93170.33340.67020.05080.05940.41650.11750.6947-51.8717-36.40654.8284
47.46773.8494-1.34765.6365-0.60810.18190.305-0.5567-0.62930.7306-0.2661-0.0045-0.0366-0.24170.02160.67190.01670.03520.38860.05360.5556-42.8149-27.27973.7109
52.99193.31361.59428.29145.5215.5056-0.85480.58360.46631.127-0.18012.55930.04322.23460.75951.2746-0.06620.53531.46320.06212.1472-52.5846-13.75848.1882
63.3813-1.15752.55334.0432-3.79496.938-0.1718-0.44930.18620.2129-0.135-0.3955-0.4673-0.26960.21210.72950.08730.1210.54290.01010.7011-40.5761-2.67221.1304
75.84950.9976-0.39781.69280.64756.84830.0260.5295-0.2960.4599-0.03110.00960.5209-0.38670.5430.75090.19720.22620.44360.17410.2579-50.794210.9222-1.5304
89.76540.7393-0.54891.59820.72948.08180.1538-0.35-0.00810.22190.2027-0.2501-0.2754-0.9188-0.20951.07060.15170.10820.56750.17080.9138-49.872215.3907-8.9856
97.0523-0.54451.43742.54550.42927.9795-0.15440.0868-0.0537-0.4602-0.37841.3808-0.81880.01050.18550.96280.2580.09140.65240.25610.849-51.030215.7782-15.6019
105.27120.4165-1.69973.5264-1.63734.88610.37120.63420.5238-0.17680.19060.8138-0.2078-0.8787-0.2530.91920.27420.08160.84580.31211.0663-53.2330.983-23.6074
111.42351.36830.79353.6578-0.48364.42740.86440.36661.65070.90610.06152.6407-0.82990.036-0.43061.41580.14550.64880.69340.20791.6111-38.54348.5482-32.0401
126.47490.635-0.23262.81741.58144.17560.09510.72320.4792-0.01570.55150.0657-0.7060.1495-0.52011.2810.03060.30310.87010.29071.1316-31.828740.4494-34.9558
132.3953-1.5888-3.60576.1059-2.00229.23790.07221.47091.0858-1.595-0.9743-1.14480.73470.46110.78041.56050.12630.44311.34670.2561.131-24.504136.005-45.1503
144.5523-0.61381.36823.45972.0375.1721-0.24611.35761.3196-0.5119-0.09870.0366-0.75340.6673-0.15071.21130.04590.38141.2574-0.05520.9066-23.876226.1077-43.548
155.50291.571-6.61495.5370.32848.9255-0.2737-0.37540.33520.1790.8775-1.3116-0.88730.0754-0.8071.29160.4938-0.11681.4882-0.19250.801-14.086720.1874-24.1208
163.089-0.66910.84313.89250.48322.2715-0.0346-0.56680.72660.3078-0.68811.0279-2.692-1.3252-0.13092.09850.69770.18021.2394-0.07950.791-22.8819.4222-20.2214
175.6046-3.74541.67348.90551.73834.0633-0.21580.558-0.1947-0.32710.511-0.71980.17290.613-0.30530.9970.08870.18950.9981-0.20840.6639-14.536810.1614-36.8523
187.10280.1355-0.71073.4354-2.88146.44910.63840.0438-0.0170.18180.0923-0.13731.4753-0.7001-0.72411.22430.02150.31681.4324-0.27511.1101-2.94130.7192-38.0962
199.0811-6.1709-5.33755.15494.10853.7745-1.6510.8585-0.47520.90531.3488-1.94321.76930.60120.40771.2397-0.05990.29711.3367-0.39151.635715.58914.0329-40.366
204.67550.9709-1.00899.72973.24855.1361-0.0996-0.5512-1.1364-0.6774-0.0786-0.5831-0.27631.09650.57171.45870.31290.24671.2646-0.12731.45234.8809-7.4878-43.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 80:90)
2X-RAY DIFFRACTION2(chain A and resid 91:200)
3X-RAY DIFFRACTION3(chain A and resid 201:264)
4X-RAY DIFFRACTION4(chain A and resid 265:355)
5X-RAY DIFFRACTION5(chain A and resid 356:363)
6X-RAY DIFFRACTION6(chain A and resid 364:423)
7X-RAY DIFFRACTION7(chain A and resid 424:468)
8X-RAY DIFFRACTION8(chain A and resid 469:502)
9X-RAY DIFFRACTION9(chain A and resid 503:557)
10X-RAY DIFFRACTION10(chain A and resid 558:651)
11X-RAY DIFFRACTION11(chain A and resid 652:675)
12X-RAY DIFFRACTION12(chain A and resid 676:755)
13X-RAY DIFFRACTION13(chain A and resid 756:777)
14X-RAY DIFFRACTION14(chain A and resid 778:823)
15X-RAY DIFFRACTION15(chain A and resid 824:852)
16X-RAY DIFFRACTION16(chain A and resid 853:861)
17X-RAY DIFFRACTION17(chain A and resid 862:930)
18X-RAY DIFFRACTION18(chain A and resid 931:984)
19X-RAY DIFFRACTION19(chain A and resid 985:998)
20X-RAY DIFFRACTION20(chain A and resid 999:1048)

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