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- PDB-6v7s: Crystal structure of K37-acetylated SUMO1 in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 6v7s
TitleCrystal structure of K37-acetylated SUMO1 in complex with phosphorylated PIAS-SIM2
Components
  • Protein PIAS
  • Small ubiquitin-related modifier 1
KeywordsPEPTIDE BINDING PROTEIN / SUMO1 / PIAS / SUMO INTERACTION MOTIF
Function / homology
Function and homology information


protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / Regulation of IFNG signaling / potassium channel regulator activity / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research74739 Canada
Canadian Institutes of Health Research130414 Canada
CitationJournal: Structure / Year: 2020
Title: Characterization of a C-Terminal SUMO-Interacting Motif Present in Select PIAS-Family Proteins.
Authors: Lussier-Price, M. / Mascle, X.H. / Cappadocia, L. / Kamada, R. / Sakaguchi, K. / Wahba, H.M. / Omichinski, J.G.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Small ubiquitin-related modifier 1
D: Protein PIAS
A: Small ubiquitin-related modifier 1
B: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)22,0484
Polymers22,0484
Non-polymers00
Water4,288238
1
C: Small ubiquitin-related modifier 1
D: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)11,0242
Polymers11,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Small ubiquitin-related modifier 1
B: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)11,0242
Polymers11,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.294, 38.457, 120.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 9567.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P63165
#2: Protein/peptide Protein PIAS


Mass: 1456.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.47→23.731 Å / Num. obs: 29982 / % possible obs: 95.9 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 10.84
Reflection shellResolution: 1.47→1.523 Å / Num. unique obs: 2009 / CC1/2: 0.378

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Processing

Software
NameVersionClassification
PHENIX1.13-2998_1496refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UYO

6uyo


Resolution: 1.47→23.731 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.91
RfactorNum. reflection% reflection
Rfree0.1925 2001 6.68 %
Rwork0.1707 --
obs0.1722 29971 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.11 Å2 / Biso mean: 26.5153 Å2 / Biso min: 11.31 Å2
Refinement stepCycle: final / Resolution: 1.47→23.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 239 1647
Biso mean---36.19 -
Num. residues----170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4704-1.50710.3314930.3408122060
1.5071-1.54790.34691200.2856174085
1.5479-1.59340.2781450.2609202098
1.5934-1.64480.29231520.22282015100
1.6448-1.70360.24551440.20542048100
1.7036-1.77180.21851430.20022038100
1.7718-1.85240.2061500.17172066100
1.8524-1.950.18671490.17092097100
1.95-2.07210.17941420.15122042100
2.0721-2.2320.21221490.16042095100
2.232-2.45640.17641520.15512091100
2.4564-2.81140.18131500.15942103100
2.8114-3.54020.16891570.16032143100
3.5402-23.7310.1741550.16142252100
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)
11.49320.39710.09472.02340.40191.72060.0506-0.1317-0.08470.12220.0229-0.14140.05190.20350.01190.1324-0.0015-0.01250.1038-0.01720.1311-10.8602-0.895932.0037
20.2664-0.2342-0.22580.4901-0.01940.3626-0.18830.39450.2022-0.4827-0.0878-0.022-0.47820.00260.00030.3344-0.0122-0.01160.2898-0.0180.2631-16.00426.975222.2009
31.89760.38440.03240.7103-0.06772.2250.0408-0.02630.06510.0344-0.05690.0451-0.11130.041100.1081-0.00940.0040.1291-0.00910.1034-2.1537-4.90826.5031
40.46520.18020.08420.4413-0.35870.4476-0.09570.17240.0689-0.3264-0.10310.0486-0.2406-0.3045-0.00190.16090.0036-0.02480.22690.01060.1722-9.3892-3.7931-5.1841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA17 - 93
2X-RAY DIFFRACTION2chain BB6 - 15
3X-RAY DIFFRACTION3chain CC21 - 93
4X-RAY DIFFRACTION4chain DD5 - 14

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