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- PDB-7zjs: Structural basis of centromeric cohesion protection by SGO1 -

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Basic information

Entry
Database: PDB / ID: 7zjs
TitleStructural basis of centromeric cohesion protection by SGO1
Components
  • Cohesin subunit SA-2
  • Double-strand-break repair protein rad21 homolog
  • Shugoshin 1
KeywordsCELL CYCLE / cohesin / STAG2 / SGO1 / HEAT
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / negative regulation of mitotic metaphase/anaphase transition / centriole-centriole cohesion / 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 ...mitotic sister chromatid cohesion, centromeric / negative regulation of mitotic metaphase/anaphase transition / centriole-centriole cohesion / 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 / meiotic chromosome segregation / negative regulation of G2/M transition of mitotic cell cycle / attachment of spindle microtubules to kinetochore / negative regulation of glial cell apoptotic process / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / condensed chromosome, centromeric region / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic spindle pole / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / kinetochore / kinase binding / nuclear matrix / fibrillar center / spindle pole / 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 / response to hypoxia / nuclear speck / cell division / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA ...Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / : / 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-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Shugoshin 1 / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsPatel, A. / Panne, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust219534/Z/19/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W001667/1 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural basis of centromeric cohesion protection.
Authors: Garcia-Nieto, A. / Patel, A. / Li, Y. / Oldenkamp, R. / Feletto, L. / Graham, J.J. / Willems, L. / Muir, K.W. / Panne, D. / Rowland, B.D.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: 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.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cohesin subunit SA-2
B: Double-strand-break repair protein rad21 homolog
C: Cohesin subunit SA-2
D: Double-strand-break repair protein rad21 homolog
E: Shugoshin 1
F: Shugoshin 1


Theoretical massNumber of molelcules
Total (without water)429,1796
Polymers429,1796
Non-polymers00
Water77543
1
A: Cohesin subunit SA-2
B: Double-strand-break repair protein rad21 homolog
E: Shugoshin 1


Theoretical massNumber of molelcules
Total (without water)214,5903
Polymers214,5903
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-34 kcal/mol
Surface area48710 Å2
MethodPISA
2
C: Cohesin subunit SA-2
D: Double-strand-break repair protein rad21 homolog
F: Shugoshin 1


Theoretical massNumber of molelcules
Total (without water)214,5903
Polymers214,5903
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-40 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.808, 181.098, 111.374
Angle α, β, γ (deg.)90.000, 94.254, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 141502.094 Da / Num. of mol.: 2
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.: 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: Protein/peptide Shugoshin 1 / Serologically defined breast cancer antigen NY-BR-85 / Shugoshin-like 1


Mass: 1315.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5FBB7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 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: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.24→47.87 Å / Num. obs: 48451 / % possible obs: 99.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 108.36 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 3.24→3.35 Å / Num. unique obs: 4517 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QNX

6qnx


Resolution: 3.24→47.87 Å / SU ML: 0.5833 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2887 2420 5 %
Rwork0.2689 45950 -
obs0.2699 48370 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.93 Å2
Refinement stepCycle: LAST / Resolution: 3.24→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16178 0 0 43 16221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006216452
X-RAY DIFFRACTIONf_angle_d0.890322171
X-RAY DIFFRACTIONf_chiral_restr0.04572527
X-RAY DIFFRACTIONf_plane_restr0.00472803
X-RAY DIFFRACTIONf_dihedral_angle_d16.97436186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.310.50381300.45882366X-RAY DIFFRACTION86.22
3.31-3.380.44821460.43772701X-RAY DIFFRACTION97.63
3.38-3.460.40221410.39292733X-RAY DIFFRACTION99
3.46-3.540.39811110.3592742X-RAY DIFFRACTION98.82
3.54-3.640.3271410.3152714X-RAY DIFFRACTION98.75
3.64-3.750.29781470.30882708X-RAY DIFFRACTION98.38
3.75-3.870.31331250.2892741X-RAY DIFFRACTION98.56
3.87-4.010.3051850.28852647X-RAY DIFFRACTION98.27
4.01-4.170.27261320.27942761X-RAY DIFFRACTION99.14
4.17-4.350.30451330.25432742X-RAY DIFFRACTION99.55
4.36-4.580.28321360.24352737X-RAY DIFFRACTION99.03
4.58-4.870.23831270.24532775X-RAY DIFFRACTION99.04
4.87-5.250.27721190.24962746X-RAY DIFFRACTION98.73
5.25-5.770.31351600.272704X-RAY DIFFRACTION98.76
5.77-6.610.32271580.30442734X-RAY DIFFRACTION98.87
6.61-8.320.26821780.24772683X-RAY DIFFRACTION98.05
8.32-47.870.22521510.21092716X-RAY DIFFRACTION96.53

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