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- PDB-6uyy: Crystal structure of K39-acetylated SUMO1 in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 6uyy
TitleCrystal structure of K39-acetylated SUMO1 in complex with phosphorylated DAXX
Components
  • Small ubiquitin-related modifier 1
  • phosphorylated DAXX
KeywordsNUCLEAR PROTEIN/PROTEIN BINDING / SUMO1 / PML / SUMO INTERACTION MOTIF / PHOSPHOSIM / NUCLEAR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding ...negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / : / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / regulation of protein stability / protein tag activity / Formation of Incision Complex in GG-NER / 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: 1.599 Å
AuthorsWahba, H.M. / Gagnon, C. / Mascle, X.H. / Lussier-Price, M. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)74739 Canada
Canadian Institutes of Health Research (CIHR)130414 Canada
CitationJournal: Structure / Year: 2020
Title: Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner.
Authors: Mascle, X.H. / Gagnon, C. / Wahba, H.M. / Lussier-Price, M. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G.
History
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 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 2.1Oct 23, 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
A: Small ubiquitin-related modifier 1
B: phosphorylated DAXX


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5692
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.523, 38.161, 49.757
Angle α, β, γ (deg.)90.000, 119.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

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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.: 1 / Mutation: C52A
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) / References: UniProt: P63165
#2: Protein/peptide phosphorylated DAXX


Mass: 2000.877 Da / Num. of mol.: 1
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.: 118 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM 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: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.599→19.081 Å / Num. obs: 11903 / % possible obs: 95.17 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 10.67
Reflection shellResolution: 1.599→1.656 Å / Num. unique obs: 901 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_1496refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJN

4wjn


Resolution: 1.599→19.081 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.1746 1191 10.01 %
Rwork0.1555 --
obs0.1574 11903 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.42 Å2 / Biso mean: 27.6282 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.599→19.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 0 118 852
Biso mean---36.04 -
Num. residues----90
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.599-1.66260.28021000.234290073
1.6626-1.73820.23821310.2051118194
1.7382-1.82980.20531350.1912121098
1.8298-1.94430.22261340.1676120598
1.9443-2.09430.18371340.1551121498
2.0943-2.30470.17561380.1426123198
2.3047-2.63740.13911370.1476124199
2.6374-3.320.18161380.1597124299
3.32-19.0810.15411440.1401128899
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)
11.59760.57050.92261.79310.37111.75620.0074-0.06510.01430.06120.0173-0.07250.021-0.0933-0.00120.11720.0037-0.00260.11350.00120.111514.7192-4.65037.9286
20.8880.0679-0.05211.10170.52160.90040.1247-0.1002-0.0320.2191-0.1801-0.10130.15960.2857-0.00510.2038-0.0138-0.01110.1984-0.0060.18867.4558-12.9591.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA19 - 97
2X-RAY DIFFRACTION2chain BB6 - 16

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