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- PDB-6qb5: Crystal structure of the N-terminal region of human cohesin subun... -

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Basic information

Entry
Database: PDB / ID: 6qb5
TitleCrystal structure of the N-terminal region of human cohesin subunit STAG1
ComponentsCohesin subunit SA-1
KeywordsGENE REGULATION / Cohesin / SA-1 / chromosome segregation
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 / chromosome, centromeric region / mitotic spindle assembly / 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 / chromosome, centromeric region / mitotic spindle assembly / 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 / nuclear body / cilium / 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: 2.02 Å
AuthorsNewman, J.A. / Katis, V.L. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
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
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Jan 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
C: Cohesin subunit SA-1
A: Cohesin subunit SA-1
B: Cohesin subunit SA-1
D: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,5415
Polymers158,5184
Non-polymers231
Water11,295627
1
C: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)39,6301
Polymers39,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)39,6301
Polymers39,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)39,6301
Polymers39,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6532
Polymers39,6301
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.611, 124.985, 231.889
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-1 / SCC3 homolog 1 / Stromal antigen 1


Mass: 39629.531 Da / Num. of mol.: 4
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na/K Phosphate pH 6.0, 0.2 M NaCl, 34% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.02→110 Å / Num. obs: 125560 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.052 / Net I/σ(I): 9.8
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9012 / CC1/2: 0.664 / Rpim(I) all: 0.583 / % possible all: 98

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Processing

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

4pk7


Resolution: 2.02→85.002 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.54
RfactorNum. reflection% reflection
Rfree0.2455 6231 4.98 %
Rwork0.2184 --
obs0.2197 125215 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→85.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9986 0 1 627 10614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00110169
X-RAY DIFFRACTIONf_angle_d0.34113712
X-RAY DIFFRACTIONf_dihedral_angle_d17.866160
X-RAY DIFFRACTIONf_chiral_restr0.0331549
X-RAY DIFFRACTIONf_plane_restr0.0021745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.04290.351820.3483882X-RAY DIFFRACTION97
2.0429-2.06690.35022130.33273797X-RAY DIFFRACTION98
2.0669-2.09220.31762040.32033774X-RAY DIFFRACTION97
2.0922-2.11860.37022030.30083982X-RAY DIFFRACTION99
2.1186-2.14650.34512220.28483833X-RAY DIFFRACTION100
2.1465-2.17590.32332080.27793956X-RAY DIFFRACTION100
2.1759-2.2070.32971730.27023962X-RAY DIFFRACTION100
2.207-2.240.32811970.2533938X-RAY DIFFRACTION99
2.24-2.2750.2842110.24593934X-RAY DIFFRACTION99
2.275-2.31230.28632210.24483890X-RAY DIFFRACTION100
2.3123-2.35210.30612090.24123970X-RAY DIFFRACTION100
2.3521-2.39490.26722030.23593904X-RAY DIFFRACTION100
2.3949-2.4410.2712140.23863949X-RAY DIFFRACTION100
2.441-2.49080.28342090.23353940X-RAY DIFFRACTION100
2.4908-2.5450.28132110.22913953X-RAY DIFFRACTION100
2.545-2.60420.26132060.22863959X-RAY DIFFRACTION100
2.6042-2.66930.26422050.223960X-RAY DIFFRACTION100
2.6693-2.74150.24982120.22093975X-RAY DIFFRACTION100
2.7415-2.82220.26892120.21813935X-RAY DIFFRACTION100
2.8222-2.91320.25322170.22263965X-RAY DIFFRACTION100
2.9132-3.01740.27232030.23143999X-RAY DIFFRACTION100
3.0174-3.13820.24871810.22794017X-RAY DIFFRACTION100
3.1382-3.2810.2432110.21994000X-RAY DIFFRACTION100
3.281-3.4540.21392020.2194001X-RAY DIFFRACTION100
3.454-3.67040.26622430.21063953X-RAY DIFFRACTION100
3.6704-3.95380.22872090.18924022X-RAY DIFFRACTION100
3.9538-4.35170.19111910.18484072X-RAY DIFFRACTION100
4.3517-4.98130.20182140.17974071X-RAY DIFFRACTION100
4.9813-6.27560.24862110.22074113X-RAY DIFFRACTION100
6.2756-85.0770.19892340.20484278X-RAY DIFFRACTION99

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