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- PDB-4fo9: Crystal structure of the E3 SUMO Ligase PIAS2 -

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Basic information

Entry
Database: PDB / ID: 4fo9
TitleCrystal structure of the E3 SUMO Ligase PIAS2
ComponentsE3 SUMO-protein ligase PIAS2Protein inhibitor of activated STAT2
KeywordsLIGASE / SUMO / E3 Ligase / PINIT domain / SP-RING domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


SUMO ligase activity / negative regulation of androgen receptor signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of ubiquitinylation proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors ...SUMO ligase activity / negative regulation of androgen receptor signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of ubiquitinylation proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / transcription coregulator activity / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / PML body / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / DNA-templated transcription / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PINIT domain / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP motif profile. ...PINIT domain / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase PIAS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsDong, A. / Hu, J. / Dobrovetsky, E. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the E3 SUMO Ligase PIAS2
Authors: Hu, J. / Dong, A. / Dobrovetsky, E. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 SUMO-protein ligase PIAS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,69522
Polymers40,6301
Non-polymers6521
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.288, 170.140, 57.507
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-516-

UNX

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Components

#1: Protein E3 SUMO-protein ligase PIAS2 / Protein inhibitor of activated STAT2 / Androgen receptor-interacting protein 3 / ARIP3 / DAB2-interacting protein / DIP / Msx-interacting ...Androgen receptor-interacting protein 3 / ARIP3 / DAB2-interacting protein / DIP / Msx-interacting zinc finger protein / Miz1 / PIAS-NY protein / Protein inhibitor of activated STAT x / Protein inhibitor of activated STAT2


Mass: 40629.980 Da / Num. of mol.: 1 / Fragment: UNP residues 147-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIAS2, PIASX / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R
References: UniProt: O75928, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 20 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.7 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7 M KH2PO4/NaH2PO4, pH6.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28295 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2012
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28295 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 17845 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.087 / Χ2: 2.015 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.447.60.8738750.9981100
2.44-2.497.80.7748701.0021100
2.49-2.537.90.6668771.025199.8
2.53-2.5980.6358831.0091100
2.59-2.6480.4768701.074199.9
2.64-2.780.458811.2011100
2.7-2.7780.3478781.0551100
2.77-2.8580.2638861.1361100
2.85-2.9380.2358851.1941100
2.93-3.0280.1848971.3131100
3.02-3.138.10.1428861.3971100
3.13-3.2680.1148801.5791100
3.26-3.4180.1089051.9481100
3.41-3.587.80.0878892.546199.9
3.58-3.817.80.0798892.9651100
3.81-4.17.60.0688963.181100
4.1-4.527.40.0629083.816199.9
4.52-5.177.40.0559133.7891100
5.17-6.517.10.0569314.1391100
6.51-506.40.0439464.769196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
REFMACrefmac_5.7.0027refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.39→32.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 13.663 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 739 4.1 %RANDOM
Rwork0.2082 ---
obs0.2103 17834 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 59.2593 Å2 / Biso min: 26.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--1.65 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.39→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 21 43 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192014
X-RAY DIFFRACTIONr_bond_other_d0.0010.021899
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9842747
X-RAY DIFFRACTIONr_angle_other_deg0.7183.0014337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88923.01473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06115317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6341515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.392-2.4540.262580.3111169127696.16
2.454-2.5220.295490.2621225127599.922
2.522-2.5950.369380.26512031241100
2.595-2.6740.285580.2441160121999.918
2.674-2.7620.268510.2291093114599.913
2.762-2.8590.368390.20510911130100
2.859-2.9670.278450.21810431088100
2.967-3.0880.217480.19710111059100
3.088-3.2250.265460.2079781024100
3.225-3.3820.239320.229932964100
3.382-3.5640.313300.20890093199.893
3.564-3.780.259440.207833877100
3.78-4.0410.193290.181790819100
4.041-4.3640.192370.16873677499.871
4.364-4.7790.134300.14669072199.861
4.779-5.3410.226190.17645664100
5.341-6.1630.451290.206541570100
6.163-7.5380.383180.256490508100
7.538-10.6190.223200.21436539497.716
10.619-85.070.282190.3220024689.024
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)
16.7281-0.1562-2.76172.17411.07733.82740.0986-0.45610.34030.08030.0378-0.0751-0.106-0.0528-0.13640.0936-0.0177-0.0030.16850.01450.036732.517542.106-0.7992
29.65454.73782.13559.55671.24674.03740.05310.14050.3043-0.0295-0.1495-0.762-0.6037-0.0040.09640.35070.0212-0.02520.12450.01920.263760.273862.9885-5.4801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 298
2X-RAY DIFFRACTION2A299 - 426

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