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- PDB-8dji: Ternary complex of SUMO1 with the SIM of PML and zinc -

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Basic information

Entry
Database: PDB / ID: 8dji
TitleTernary complex of SUMO1 with the SIM of PML and zinc
Components
  • Protein PML
  • Small ubiquitin-related modifier 1
KeywordsNUCLEAR PROTEIN / SUMO1 / PML Nuclear Bodies / Zinc / auto-inhibition / Daxx
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 / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / suppression of viral release by host / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed ...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 / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / suppression of viral release by host / : / 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 / SUMO binding / small protein activating enzyme binding / positive regulation of apoptotic process involved in mammary gland involution / fibroblast migration / SMAD protein signal transduction / myeloid cell differentiation / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / protein-containing complex localization / maintenance of protein location in nucleus / XY body / regulation of calcium ion transmembrane transport / endoplasmic reticulum calcium ion homeostasis / Maturation of nucleoprotein / regulation of double-strand break repair / branching involved in mammary gland duct morphogenesis / SUMOylation of RNA binding proteins / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / Maturation of nucleoprotein / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / entrainment of circadian clock by photoperiod / transcription factor binding / SMAD binding / ubiquitin-specific protease binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / 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 / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cell fate commitment / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / protein targeting / negative regulation of DNA-binding transcription factor activity / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / presynaptic cytosol / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of cell growth / regulation of circadian rhythm / PML body / PKR-mediated signaling
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / 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 ...Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / 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: 1.97 Å
AuthorsLussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)70439, 130414 and 166104 Canada
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1.
Authors: Lussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2175
Polymers14,0202
Non-polymers1963
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-91 kcal/mol
Surface area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.995, 47.156, 63.777
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: 11043.335 Da / Num. of mol.: 1
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 / E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 ...E3 SUMO-protein ligase PML / Promyelocytic leukemia protein / RING finger protein 71 / RING-type E3 SUMO transferase PML / Tripartite motif-containing protein 19 / TRIM19


Mass: 2976.985 Da / Num. of mol.: 1 / Fragment: SIM
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, Transferases; Acyltransferases; Aminoacyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.97→32 Å / Num. obs: 14192 / % possible obs: 96.58 % / Redundancy: 5.5 % / CC1/2: 0.982 / Net I/σ(I): 5.34
Reflection shellResolution: 1.97→2.044 Å / Num. unique obs: 637 / CC1/2: 0.263

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7P

6v7p


Resolution: 1.97→32 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1443 10.17 %
Rwork0.2308 12749 -
obs0.2336 14192 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.06 Å2 / Biso mean: 34.7233 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.97→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 3 60 797
Biso mean--44.5 38.04 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.040.3614910.347786295362
2.04-2.130.39241290.33151077120681
2.13-2.220.29441440.30051292143695
2.22-2.340.3391550.2751355151099
2.34-2.490.32571540.256613661520100
2.49-2.680.23421560.243113501506100
2.68-2.950.27151540.240913661520100
2.95-3.370.25291500.202213791529100
3.37-4.250.19761490.178113471496100
4.25-320.23611610.218813551516100
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)
11.0095-0.49310.6731.33160.13710.9263-0.03430.0462-0.07120.04290.0230.03890.03830.1081-0.00010.3143-0.02710.01210.26840.00470.24360.95077.24646.7637
20.24930.12980.15360.3063-0.11030.2789-0.0221-0.0884-0.0149-0.25080.02030.1499-0.05620.1020.00540.283-0.02420.02140.3896-0.01720.3412-7.031318.09049.7802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA19 - 93
2X-RAY DIFFRACTION2chain BB7 - 29

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