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- PDB-6v7r: Crystal structure of K37-acetylated SUMO1 in complex with PIAS-SIM2 -

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Basic information

Entry
Database: PDB / ID: 6v7r
TitleCrystal structure of K37-acetylated SUMO1 in complex with PIAS-SIM2
Components
  • Protein PIAS
  • Small ubiquitin-related modifier 1
KeywordsPEPTIDE BINDING PROTEIN / SUMO1 / PIAS / SUMO INTERACTION MOTIF
Function / homology
Function and homology information


negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding ...negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / protein stabilization / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / 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-like domain / Ubiquitin domain profile. / 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: 1.549 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

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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)21,8894
Polymers21,8894
Non-polymers00
Water3,153175
1
C: Small ubiquitin-related modifier 1
D: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)10,9442
Polymers10,9442
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)10,9442
Polymers10,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.100, 38.246, 121.053
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: 1376.449 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 / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.95 %
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 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: 1.549→30.263 Å / Num. obs: 24975 / % possible obs: 93.95 % / Redundancy: 5.7 % / CC1/2: 0.997 / Net I/σ(I): 12.23
Reflection shellResolution: 1.549→1.604 Å / Num. unique obs: 1492 / CC1/2: 0.501

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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: 1.549→30.263 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2212 2011 8.05 %
Rwork0.1823 --
obs0.1855 24973 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.86 Å2 / Biso mean: 35.1703 Å2 / Biso min: 15.89 Å2
Refinement stepCycle: final / Resolution: 1.549→30.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 0 176 1571
Biso mean---39.97 -
Num. residues----169
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.549-1.58730.39780.340291653
1.5873-1.63020.39131090.3184121873
1.6302-1.67810.34071350.2879155389
1.6781-1.73230.32391480.2573169199
1.7323-1.79420.26481550.23861705100
1.7942-1.8660.26691500.21181723100
1.866-1.95090.23221520.1891735100
1.9509-2.05380.21271500.17021721100
2.0538-2.18240.23821540.17921733100
2.1824-2.35090.24921540.17071766100
2.3509-2.58730.20831540.1731740100
2.5873-2.96150.22241510.19141775100
2.9615-3.730.22561560.16411784100
3.73-30.2630.17171650.16591902100
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)
11.7290.13340.10123.45830.84392.11950.0683-0.1098-0.11550.20660.0886-0.210.04870.3270.01260.2476-0.005-0.01430.1986-0.03570.2443-10.8259-0.976832.0142
20.8131-0.113-0.1550.03660.12970.8580.2996-0.02990.1221-0.6202-0.1688-0.0017-0.4158-0.32520.09560.4449-0.01290.02540.4012-0.06350.4949-14.88317.184323.5516
32.71040.6770.44711.3873-0.14522.88250.0366-0.11780.12640.0589-0.0720.0458-0.13920.0645-0.00020.1774-0.01490.01450.2022-0.02470.1771-2.1409-4.88086.5481
40.49190.0470.14520.6885-0.44190.3509-0.31520.02760.048-0.0867-0.00720.2217-0.05280.0238-0.00120.23870.0103-0.02250.3327-0.00640.2573-8.7265-4.3359-5.9786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA17 - 93
2X-RAY DIFFRACTION2chain BB8 - 15
3X-RAY DIFFRACTION3chain CC20 - 93
4X-RAY DIFFRACTION4chain DD5 - 14

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