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- PDB-6rrc: Crystal structure of the N-terminal region of human cohesin subun... -

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Basic information

Entry
Database: PDB / ID: 6rrc
TitleCrystal structure of the N-terminal 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 / SA-1 / chromosome segregation
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 / Estrogen-dependent gene expression / DNA-binding transcription factor binding / 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: 2.37 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 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 1, 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 1.3Aug 19, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,4428
Polymers85,0584
Non-polymers3844
Water1,17165
1
C: Cohesin subunit SA-1
B: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9136
Polymers42,5292
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-46 kcal/mol
Surface area18410 Å2
MethodPISA
2
A: Cohesin subunit SA-1
D: Double-strand-break repair protein rad21 homolog


Theoretical massNumber of molelcules
Total (without water)42,5292
Polymers42,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-3 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.077, 151.662, 126.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 39629.531 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: 2899.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60216
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3

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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 PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.37→75.83 Å / Num. obs: 46073 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Net I/σ(I): 14
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2213 / CC1/2: 0.705 / Rpim(I) all: 0.543 / % possible all: 97.9

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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: 2.37→74.792 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.2483 2295 4.99 %
Rwork0.2136 --
obs0.2154 46007 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.37→74.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 20 65 5659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025674
X-RAY DIFFRACTIONf_angle_d0.3867646
X-RAY DIFFRACTIONf_dihedral_angle_d20.6073450
X-RAY DIFFRACTIONf_chiral_restr0.033863
X-RAY DIFFRACTIONf_plane_restr0.002976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3688-2.42030.35271420.33522639X-RAY DIFFRACTION98
2.4203-2.47660.32091400.31182687X-RAY DIFFRACTION100
2.4766-2.53850.33591270.30192728X-RAY DIFFRACTION100
2.5385-2.60720.32861600.29472693X-RAY DIFFRACTION100
2.6072-2.68390.28161290.28062719X-RAY DIFFRACTION100
2.6839-2.77050.29121480.26212679X-RAY DIFFRACTION100
2.7705-2.86950.29221430.25432714X-RAY DIFFRACTION100
2.8695-2.98440.30211420.26742734X-RAY DIFFRACTION100
2.9844-3.12030.31291250.27232721X-RAY DIFFRACTION100
3.1203-3.28480.30541310.2592758X-RAY DIFFRACTION100
3.2848-3.49060.29461330.24112734X-RAY DIFFRACTION100
3.4906-3.76010.28361450.21682738X-RAY DIFFRACTION100
3.7601-4.13850.20261530.18192732X-RAY DIFFRACTION100
4.1385-4.73720.20751440.17242779X-RAY DIFFRACTION100
4.7372-5.9680.25741660.20422771X-RAY DIFFRACTION100
5.968-74.82920.20671670.18412886X-RAY DIFFRACTION100
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)
13.13850.72960.53354.96080.37114.9481-0.02130.2551-0.5144-0.15580.1123-0.23060.79480.1663-0.08240.85880.0660.02240.6696-0.1940.682827.05954.209612.8874
20.8440.33120.55585.5554-2.56783.55610.05810.3145-0.087-0.15050.05240.3318-0.0057-0.0927-0.1470.54690.0722-0.00490.6588-0.11240.54522.857223.804619.2403
35.1258-2.1963.86473.0124-0.99167.33190.05190.04750.10460.1803-0.1548-0.11240.05870.03920.11640.55-0.0060.02150.4921-0.03620.504831.308721.554941.6737
47.7933-0.48811.67458.7366-1.85039.36740.4304-0.3074-1.9041.7408-0.13110.23410.36640.5142-0.27540.87080.1378-0.13341.03550.03521.197840.419347.455247.749
59.13541.93174.1919.8384-2.81046.3640.2497-0.0393-1.0420.57760.04050.07942.1067-0.6493-0.26251.3615-0.1758-0.04820.9833-0.02260.790721.8129-4.596132.3253
65.3163-4.50882.87284.8133-3.43223.23830.41180.6656-0.3388-0.6911-1.1455-0.9251.1221-0.71380.53692.11130.14590.42411.7030.36571.278318.55617.132246.4699
74.06421.28060.64863.7011-0.44252.4371-0.27810.83830.9058-0.5335-0.03760.0683-0.27410.23980.35750.880.0453-0.10750.88970.20660.755558.612332.814739.579
80.35171.3388-0.66027.3738-2.08181.9022-0.29680.1632-0.0467-1.33660.22770.96880.247-0.4657-0.05641.21210.0365-0.12741.0491-0.08620.886655.05877.240238.347
96.784.14050.06057.53490.21534.3004-0.18770.29790.5291-0.2698-0.008-0.3337-0.59740.46620.20850.79550.002-0.02290.69020.13690.713371.674327.882650.1951
104.3374-0.47262.68161.06381.28965.9172-0.12490.16890.19020.0595-0.1254-0.15710.09690.10810.31040.6430.0157-0.02290.51360.03720.650673.672619.959963.1793
115.02251.44720.20864.88380.59236.3893-0.4011.00990.65740.3603-0.3566-1.7693-1.0040.45450.73591.2474-0.2035-0.09851.21470.37721.488979.801141.665942.5848
126.0263-1.895-1.17556.72286.57566.52440.032-0.8544-0.6154-0.23470.6173-0.3431-0.09420.5939-0.81691.7158-0.1892-0.10051.43740.17961.648689.096525.226552.4639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 84 through 215 )
2X-RAY DIFFRACTION2chain 'C' and (resid 216 through 321 )
3X-RAY DIFFRACTION3chain 'C' and (resid 322 through 402 )
4X-RAY DIFFRACTION4chain 'C' and (resid 403 through 419 )
5X-RAY DIFFRACTION5chain 'B' and (resid 322 through 333 )
6X-RAY DIFFRACTION6chain 'B' and (resid 334 through 339 )
7X-RAY DIFFRACTION7chain 'A' and (resid 85 through 255 )
8X-RAY DIFFRACTION8chain 'A' and (resid 256 through 294 )
9X-RAY DIFFRACTION9chain 'A' and (resid 295 through 321 )
10X-RAY DIFFRACTION10chain 'A' and (resid 322 through 408 )
11X-RAY DIFFRACTION11chain 'D' and (resid 322 through 333 )
12X-RAY DIFFRACTION12chain 'D' and (resid 334 through 345 )

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