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- PDB-8djh: Ternary complex of SUMO1 with a phosphomimetic SIM of PML and zinc -

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Basic information

Entry
Database: PDB / ID: 8djh
TitleTernary complex of SUMO1 with a phosphomimetic SIM of PML and zinc
Components
  • PML 4SD
  • Small ubiquitin-related modifier 1
KeywordsNUCLEAR PROTEIN / SUMO1 / PML Nuclear Bodies / Zinc / auto-inhibition / Daxx
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 immune response proteins / SUMOylation of SUMOylation 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 / roof of mouth development / SUMOylation of ubiquitinylation proteins / 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 / Regulation of IFNG signaling / nuclear pore / 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 / MOLECULAR REPLACEMENT / Resolution: 1.77 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

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: PML 4SD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3946
Polymers14,1322
Non-polymers2624
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-129 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.776, 47.460, 63.632
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 PML 4SD


Mass: 3089.025 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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.77→38.04 Å / Num. obs: 19762 / % possible obs: 97.23 % / Redundancy: 3 % / CC1/2: 0.996 / Net I/σ(I): 12.02
Reflection shellResolution: 1.77→1.835 Å / Num. unique obs: 972 / CC1/2: 0.75

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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: 1.77→38.04 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 1976 10 %
Rwork0.2128 17786 -
obs0.2159 19762 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.13 Å2 / Biso mean: 19.1192 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 1.77→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 4 128 986
Biso mean--29.82 26.35 -
Num. residues----105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.820.3259990.2774939103868
1.82-1.870.24931350.26371276141193
1.87-1.920.47221460.34541293143993
1.92-1.980.28871530.27181337149096
1.98-2.050.25891520.22431306145896
2.05-2.140.2241470.20691345149297
2.14-2.230.24941390.22481335147494
2.23-2.350.37141330.27591251138492
2.35-2.50.21441510.19391330148195
2.5-2.690.22341370.181290142795
2.69-2.960.24021440.18731312145694
2.96-3.390.21251510.17951290144194
3.39-4.260.18151450.1651243138891
4.27-38.040.20431440.20661239138390
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)
11.3702-0.21330.18611.73880.08331.28030.0370.0098-0.05450.0728-0.0120.08470.1095-0.16140.11910.0381-0.016-0.0050.04290.01150.0596-0.22887.72418.5711
20.3172-0.2809-0.00533.04260.37222.2531-0.06080.01160.00730.4059-0.0370.48930.0335-0.4721-0.1140.1189-0.0140.01090.1298-0.01230.1624-8.948216.63210.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA10 - 94
2X-RAY DIFFRACTION2chain BB7 - 29

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