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

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Basic information

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


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / 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 / SUMO binding / small protein activating enzyme binding / negative regulation of action potential / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / myeloid cell differentiation / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / maintenance of protein location in nucleus / protein-containing complex localization / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / oncogene-induced cell senescence / branching involved in mammary gland duct morphogenesis / Regulation of RUNX1 Expression and Activity / positive regulation of extrinsic apoptotic signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / cobalt ion binding / Maturation of nucleoprotein / negative regulation of interleukin-1 beta production / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / transcription factor binding / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / positive regulation of signal transduction by p53 class mediator / postsynaptic cytosol / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of ubiquitin-dependent protein catabolic process / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / protein targeting / regulation of cell adhesion / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / response to UV / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / Transcriptional and post-translational regulation of MITF-M expression and activity / response to cytokine / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN localization / DNA damage response, signal transduction by p53 class mediator / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / response to gamma radiation / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...Protein of unknown function DUF3583 / PML-like, coiled-coil / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein PML / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 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 9, 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

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: Protein PML


Theoretical massNumber of molelcules
Total (without water)12,8652
Polymers12,8652
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-6 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.458, 46.942, 62.385
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.: 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 Protein PML / Promyelocytic leukemia protein / RING finger protein 71 / Tripartite motif-containing protein 19


Mass: 3296.901 Da / Num. of mol.: 1 / Mutation: E574Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Production host: Escherichia coli (E. coli) / References: UniProt: P29590
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100MM SODIUM CACODYLATE PH6.5, 16% 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 PILATUS 6M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.662→24.23 Å / Num. obs: 13664 / % possible obs: 98.79 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 10.28
Reflection shellResolution: 1.662→1.722 Å / Num. unique obs: 1279 / CC1/2: 0.391

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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: 1.662→24.226 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.57
RfactorNum. reflection% reflection
Rfree0.2004 1367 10 %
Rwork0.1708 --
obs0.1739 13664 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.16 Å2 / Biso mean: 31.1326 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 1.662→24.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 0 95 856
Biso mean---38.07 -
Num. residues----92
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.662-1.72120.30661270.2762114595
1.7212-1.79010.29311330.2453119598
1.7901-1.87150.26621340.2167120798
1.8715-1.97010.25851330.1857120499
1.9701-2.09350.21551380.1635123199
2.0935-2.2550.1741360.1561123199
2.255-2.48180.17861380.1452123599
2.4818-2.84040.1911370.15561236100
2.8404-3.57680.1871420.16171276100
3.5768-24.2260.18661490.17061337100
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)
10.7878-0.2642-0.38710.4171-0.2240.6009-0.07250.00350.16690.21140.1243-0.470.03860.29860.00980.2286-0.0069-0.0310.22030.00860.2718.41119.55627.6892
20.03160.01940.0230.0445-0.00230.05540.26270.19990.1927-0.06020.08210.72440.1308-0.5298-0.00620.47960.05370.00490.7071-0.11860.665929.998728.855814.0907
31.6873-0.3172-0.41832.07840.20610.77380.0350.00790.06930.0916-0.00340.036-0.04930.024100.1504-0.01290.00570.15140.00020.1451-0.760516.72996.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 17 )B7 - 17
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 29 )B24 - 29
3X-RAY DIFFRACTION3chain AA19 - 93

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