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- PDB-6r7o: Crystal structure of the central region of human cohesin subunit STAG1 -

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Basic information

Entry
Database: PDB / ID: 6r7o
TitleCrystal structure of the central region of human cohesin subunit STAG1
ComponentsCohesin subunit SA-1
KeywordsGENE REGULATION / cohesin / Stromal antigen / chromatid
Function / homology
Function and homology information


Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / mitotic spindle assembly / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins ...Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / mitotic spindle assembly / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / nuclear matrix / Separation of Sister Chromatids / chromosome / Estrogen-dependent gene expression / cilium / nuclear body / cell division / chromatin binding / chromatin / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / 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. / Armadillo-type fold
Similarity search - Domain/homology
Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNewman, J.A. / katis, V.L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Life Sci Alliance / Year: 2020
Title: STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
Authors: van der Lelij, P. / Newman, J.A. / Lieb, S. / Jude, J. / Katis, V. / Hoffmann, T. / Hinterndorfer, M. / Bader, G. / Kraut, N. / Pearson, M.A. / Peters, J.M. / Zuber, J. / Gileadi, O. / Petronczki, M.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 19, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cohesin subunit SA-1
B: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)105,5062
Polymers105,5062
Non-polymers00
Water3,315184
1
A: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)52,7531
Polymers52,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)52,7531
Polymers52,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.654, 166.718, 46.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 52752.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAG1, SA1, SCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVM7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.31→113.36 Å / Num. obs: 54404 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Net I/σ(I): 11.2
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3991 / CC1/2: 0.632 / Rpim(I) all: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pk7

4pk7


Resolution: 2.31→113.36 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.43
RfactorNum. reflection% reflection
Rfree0.2642 2726 5.02 %
Rwork0.2263 --
obs0.2282 54300 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→113.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 0 184 7088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017026
X-RAY DIFFRACTIONf_angle_d0.3759499
X-RAY DIFFRACTIONf_dihedral_angle_d15.4294267
X-RAY DIFFRACTIONf_chiral_restr0.0331102
X-RAY DIFFRACTIONf_plane_restr0.0031205

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