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- PDB-4pk7: crystal structure of human Stromal Antigen 2 (SA2) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4pk7
Titlecrystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins
Components
  • Cohesin subunit SA-2
  • Double-strand-break repair protein rad21 homolog
KeywordsCELL CYCLE / Sister chromatid cohesion / cohesin subunits / protein-protein interaction / HEAT repeat
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 / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process ...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 / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process / 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 / 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 / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / nuclear matrix / fibrillar center / spindle pole / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHara, K. / Chen, Z. / Tomchick, D.R. / Yu, H.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP110465 United States
Welch FoundationI-1441 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion.
Authors: Hara, K. / Zheng, G. / Qu, Q. / Liu, H. / Ouyang, Z. / Chen, Z. / Tomchick, D.R. / Yu, H.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Nov 20, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: 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_hist
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
A: Cohesin subunit SA-2
B: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9483
Polymers131,7532
Non-polymers1951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-29 kcal/mol
Surface area46760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.455, 107.275, 180.103
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-2 / SCC3 homolog 2 / Stromal antigen 2


Mass: 114980.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAG2, SA2 / Plasmid: pFastBac HT / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N3U4
#2: Protein Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 16772.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60216
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 32876 / Num. obs: 32876 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 19
Reflection shellResolution: 2.95→3 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PJU

4pju


Resolution: 2.95→47.677 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1642 5.01 %Random selection
Rwork0.1877 ---
obs0.1908 32803 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.1 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 12 0 7986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098120
X-RAY DIFFRACTIONf_angle_d1.20510936
X-RAY DIFFRACTIONf_dihedral_angle_d16.2443059
X-RAY DIFFRACTIONf_chiral_restr0.061251
X-RAY DIFFRACTIONf_plane_restr0.0041369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9469-3.03360.35181330.26422509X-RAY DIFFRACTION99
3.0336-3.13150.31211340.22782556X-RAY DIFFRACTION100
3.1315-3.24330.31161360.2112578X-RAY DIFFRACTION100
3.2433-3.37320.28371340.20182545X-RAY DIFFRACTION100
3.3732-3.52660.31361350.20592569X-RAY DIFFRACTION100
3.5266-3.71250.24781360.19892582X-RAY DIFFRACTION100
3.7125-3.9450.2561370.17742589X-RAY DIFFRACTION100
3.945-4.24940.26871360.16692582X-RAY DIFFRACTION100
4.2494-4.67670.24241380.15992627X-RAY DIFFRACTION100
4.6767-5.35270.22011360.1672610X-RAY DIFFRACTION100
5.3527-6.74080.27441410.21842655X-RAY DIFFRACTION100
6.7408-47.68340.19341460.1782759X-RAY DIFFRACTION99
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)
11.51090.63750.56630.54430.08980.4821-0.08020.07310.08240.00690.02780.037-0.05090.0234-00.1568-0.0033-0.00050.1474-0.05340.16245.5407145.805784.886
20.54050.16660.06971.00520.53970.07420.03550.0497-0.0140.16720.0606-0.16120.05230.0548-00.26290.0484-0.03920.2161-0.0290.217347.967799.817183.615
31.0203-0.46350.49970.8967-0.10170.2373-0.09690.0714-0.04690.02410.23510.0429-0.0138-0.0783-00.33140.0615-0.02160.41210.06940.250520.296786.127153.9864
40.1572-0.0055-0.02360.04470.05680.05760.0097-0.04150.05260.0420.0980.40790.08230.0365-00.27850.00520.0180.2824-0.02650.335723.6034129.926885.9116
5-0.0235-0.01050.017-0.00720.01330.00550.1536-0.13820.26540.0619-0.19080.11560.03150.079700.3839-0.0307-0.01730.2952-0.00240.440632.250499.727880.9187
60.00450.0116-0.00040.0096-0.0213-0.00040.07540.21460.08390.06350.0205-0.0296-0.09950.0439-00.42430.0509-0.06280.3829-0.1120.406334.858290.276869.1544
70.09470.0907-0.0260.0611-0.01080.047-0.40020.2090.0570.24110.1539-0.4868-0.32140.02400.38860.0524-0.04170.49060.03410.282134.040488.439452.4231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 318 )
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 605 )
3X-RAY DIFFRACTION3chain 'A' and (resid 606 through 1047 )
4X-RAY DIFFRACTION4chain 'B' and (resid 321 through 347 )
5X-RAY DIFFRACTION5chain 'B' and (resid 348 through 357 )
6X-RAY DIFFRACTION6chain 'B' and (resid 358 through 366 )
7X-RAY DIFFRACTION7chain 'B' and (resid 367 through 396 )

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