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

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Basic information

Entry
Database: PDB / ID: 4pjw
Titlecrystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1), with bound MES
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: 2.85 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 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 15, 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 / 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)131,8713
Polymers131,6762
Non-polymers1951
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-25 kcal/mol
Surface area46460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.733, 108.045, 180.835
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: 115439.008 Da / Num. of mol.: 1 / Fragment: UNP residues 80-1060
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: 16237.192 Da / Num. of mol.: 1 / Fragment: UNP residues 281-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1 / Plasmid: pFastBac HT / Cell line (production host): High Five / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.53 %
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: Oct 19, 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: 2.85→50 Å / Num. all: 37638 / Num. obs: 37638 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 79.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.1
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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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: 2.85→41.705 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1837 5 %Random selection
Rwork0.2096 ---
obs0.2104 36729 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.4 Å2
Refinement stepCycle: LAST / Resolution: 2.85→41.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 12 14 8000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058130
X-RAY DIFFRACTIONf_angle_d0.86910952
X-RAY DIFFRACTIONf_dihedral_angle_d15.5493063
X-RAY DIFFRACTIONf_chiral_restr0.0491250
X-RAY DIFFRACTIONf_plane_restr0.0031374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9270.31571390.31512638X-RAY DIFFRACTION100
2.927-3.01310.29071390.26792636X-RAY DIFFRACTION100
3.0131-3.11040.31291390.25712644X-RAY DIFFRACTION100
3.1104-3.22150.2991380.25782629X-RAY DIFFRACTION100
3.2215-3.35040.27761410.23612676X-RAY DIFFRACTION100
3.3504-3.50280.25041400.2242651X-RAY DIFFRACTION100
3.5028-3.68740.2491410.2012668X-RAY DIFFRACTION100
3.6874-3.91830.21061400.18892680X-RAY DIFFRACTION100
3.9183-4.22050.21911410.17882672X-RAY DIFFRACTION100
4.2205-4.64480.16241430.17082714X-RAY DIFFRACTION100
4.6448-5.31570.20471420.18342709X-RAY DIFFRACTION100
5.3157-6.69280.23071450.24522738X-RAY DIFFRACTION100
6.6928-41.70950.21411490.20972837X-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)
12.73760.6832-0.79841.2708-0.06370.9107-0.12160.1371-0.32270.02790.1230.04260.1375-0.10290.02570.1273-0.0035-0.01780.13890.12450.1951-45.8899-38.8729-4.7316
20.5129-0.0066-0.12271.6691-0.56690.50870.11080.20140.06140.27610.02470.3773-0.2836-0.45-0.11250.21910.2210.10410.09470.18980.2748-48.06997.2381-6.4575
32.5582-0.8161-0.67751.43060.07071.0318-0.03690.50840.1792-0.16910.3272-0.1589-0.11170.2782-0.07730.4020.11020.10780.6603-0.09630.2041-19.931421.154-36.1783
41.1158-0.20090.15721.17650.27410.4932-0.07760.1417-0.168-0.0170.1792-0.29490.0251-0.0636-0.21160.12770.05910.11080.28220.04070.3214-23.724-22.9121-4.1746
51.2198-0.56260.10240.7594-0.66321.29730.1880.3601-0.16650.0145-0.02430.276-0.0442-0.45360.17350.28970.08730.06490.36760.11180.208-33.945116.7208-28.5471
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 1048 )
4X-RAY DIFFRACTION4chain 'B' and (resid 321 through 347 )
5X-RAY DIFFRACTION5chain 'B' and (resid 348 through 395 )

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