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- PDB-6rrk: Crystal structure of the central region of human cohesin subunit ... -

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Basic information

Entry
Database: PDB / ID: 6rrk
TitleCrystal structure of the central region of human cohesin subunit STAG1 in complex with RAD21 peptide
Components
  • Cohesin subunit SA-1
  • Double-strand-break repair protein rad21 homolog
KeywordsGENE REGULATION / cohesin / Stromal antigen / chromatid
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 / 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 ...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 / 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 / chromosome segregation / nuclear matrix / 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 body / cilium / cell division / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / membrane / 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. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic ...: / 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 / Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,8954
Polymers114,8954
Non-polymers00
Water00
1
B: Cohesin subunit SA-1
D: Double-strand-break repair protein rad21 homolog


Theoretical massNumber of molelcules
Total (without water)57,4482
Polymers57,4482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-19 kcal/mol
Surface area22510 Å2
MethodPISA
2
A: Cohesin subunit SA-1
C: Double-strand-break repair protein rad21 homolog


Theoretical massNumber of molelcules
Total (without water)57,4482
Polymers57,4482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-18 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.333, 86.290, 118.585
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211

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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: Protein/peptide Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 4694.692 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60216

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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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 16 % PEG 3350, 0.2 M DL-Mallic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 3.17→69.67 Å / Num. obs: 24764 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Net I/σ(I): 7.3
Reflection shellResolution: 3.17→3.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4500 / CC1/2: 0.914 / Rpim(I) all: 0.265 / % possible all: 97.8

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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: 3.17→60.229 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 1180 4.79 %
Rwork0.2187 --
obs0.2215 24652 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.17→60.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 0 0 7289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027419
X-RAY DIFFRACTIONf_angle_d0.51810036
X-RAY DIFFRACTIONf_dihedral_angle_d16.0444502
X-RAY DIFFRACTIONf_chiral_restr0.0351171
X-RAY DIFFRACTIONf_plane_restr0.0031270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.31430.42771410.39052938X-RAY DIFFRACTION97
3.3143-3.4890.42991500.32942905X-RAY DIFFRACTION97
3.489-3.70760.3631530.28012941X-RAY DIFFRACTION97
3.7076-3.99380.30051370.23372920X-RAY DIFFRACTION97
3.9938-4.39560.27131680.20032928X-RAY DIFFRACTION96
4.3956-5.03130.24271500.19092934X-RAY DIFFRACTION97
5.0313-6.33790.31061390.24182951X-RAY DIFFRACTION96
6.3379-60.23960.21371420.17062955X-RAY DIFFRACTION94

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