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- PDB-6uyu: Crystal structure of K45-acetylated SUMO1 in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 6uyu
TitleCrystal structure of K45-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 / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / protein localization to nuclear pore / suppression of viral release by host / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins ...regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / protein localization to nuclear pore / suppression of viral release by host / 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 / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / SUMO binding / small protein activating enzyme binding / septin ring / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / negative regulation of telomerase activity / regulation of calcium ion transmembrane transport / regulation of double-strand break repair / SUMOylation of DNA methylation proteins / myeloid cell differentiation / positive regulation of telomere maintenance / SMAD protein signal transduction / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / maintenance of protein location in nucleus / protein-containing complex localization / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / endoplasmic reticulum calcium ion homeostasis / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / positive regulation of extrinsic apoptotic signaling pathway / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / 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 / cobalt ion binding / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein ligase binding / negative regulation of DNA binding / entrainment of circadian clock by photoperiod / SMAD binding / protein monoubiquitination / positive regulation of signal transduction by p53 class mediator / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / potassium channel regulator activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / cell fate commitment / protein targeting / cellular response to interleukin-4 / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / response to UV / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / Regulation of TP53 Activity through Acetylation / cellular response to cadmium ion / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / cellular response to leukemia inhibitory factor / response to cytokine / response to gamma radiation / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / regulation of circadian rhythm / negative regulation of cell growth / negative regulation of DNA-binding transcription factor activity / PML body
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / : / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / B-box zinc finger / 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 / : / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / B-box zinc finger / 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: 1.66 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 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.0Nov 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
A: Small ubiquitin-related modifier 1
B: Protein PML
C: Small ubiquitin-related modifier 1
D: Protein PML


Theoretical massNumber of molelcules
Total (without water)25,7294
Polymers25,7294
Non-polymers00
Water3,711206
1
A: Small ubiquitin-related modifier 1
B: Protein PML


Theoretical massNumber of molelcules
Total (without water)12,8652
Polymers12,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area5960 Å2
MethodPISA
2
C: Small ubiquitin-related modifier 1
D: Protein PML


Theoretical massNumber of molelcules
Total (without water)12,8652
Polymers12,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-7 kcal/mol
Surface area5620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.536, 63.136, 91.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / 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.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.658→37.014 Å / Num. obs: 25859 / % possible obs: 95.13 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 12.68
Reflection shellResolution: 1.658→1.717 Å / Num. unique obs: 1821 / CC1/2: 0.999

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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: 1.66→37.01 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.186 2000 7.74 %
Rwork0.169 --
obs0.171 25855 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 1.66→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 0 206 1670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.658-1.6990.3664950.32731126X-RAY DIFFRACTION65
1.699-1.7450.33641170.29311403X-RAY DIFFRACTION79
1.745-1.79630.27971370.22411630X-RAY DIFFRACTION93
1.7963-1.85430.22131440.19441721X-RAY DIFFRACTION97
1.8543-1.92060.19681460.17841754X-RAY DIFFRACTION99
1.9206-1.99740.18871490.171764X-RAY DIFFRACTION99
1.9974-2.08830.20441460.1651742X-RAY DIFFRACTION99
2.0883-2.19840.19651490.1651780X-RAY DIFFRACTION99
2.1984-2.33620.18231480.14931766X-RAY DIFFRACTION100
2.3362-2.51650.18381500.15831789X-RAY DIFFRACTION100
2.5165-2.76970.18851520.16411812X-RAY DIFFRACTION100
2.7697-3.17020.171510.17181804X-RAY DIFFRACTION100
3.1702-3.99340.17131540.15111834X-RAY DIFFRACTION100
3.9934-37.0140.15891620.16591930X-RAY DIFFRACTION100
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)
11.90050.82660.48332.19610.30141.5586-0.06420.0627-0.1173-0.14480.0879-0.0430.04870.05420.00840.1172-0.00220.00630.1163-0.00480.11740.925510.5183-6.1462
21.70030.45380.33941.1895-0.8491.19-0.11360.1747-0.2844-0.23050.1521-0.20470.00910.3476-0.01260.16740.00070.0310.2379-0.03240.25099.532117.4898-7.567
32.68950.1213-0.1712.10250.20721.94050.05490.218-0.062-0.1345-0.02730.0276-0.0016-0.06480.00020.13260.01770.00730.1401-0.00740.12972.3576-17.3315-8.028
40.8717-0.08350.4011.3648-0.46660.3194-0.08970.27420.248-0.46720.0393-0.25130.02990.1647-0.02140.2126-0.02310.04610.24190.00580.225211.4803-10.8262-7.4672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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