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- PDB-6uyz: Crystal structure of K46-acetylated SUMO1 in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 6uyz
TitleCrystal structure of K46-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 / XY body / SUMOylation of SUMOylation proteins / 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 / negative regulation of DNA-binding transcription factor 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: 1.4 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 / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / 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 / refine / refine_hist / refine_ls_shell / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_asym_id ..._atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _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_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _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
Revision 3.1Oct 16, 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
C: Small ubiquitin-related modifier 1
D: phosphorylated DAXX


Theoretical massNumber of molelcules
Total (without water)23,1374
Polymers23,1374
Non-polymers00
Water5,368298
1
A: Small ubiquitin-related modifier 1
B: phosphorylated DAXX


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area5400 Å2
MethodPISA
2
C: Small ubiquitin-related modifier 1
D: phosphorylated DAXX


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-4 kcal/mol
Surface area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.224, 38.316, 67.721
Angle α, β, γ (deg.)90.00, 119.91, 90.00
Int Tables number5
Space group name H-MC121

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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 phosphorylated DAXX


Mass: 2000.877 Da / Num. of mol.: 2
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.: 298 / Source method: obtained synthetically / 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: 2.44 Å3/Da / Density % sol: 49.5 %
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: 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: 1.4→48.275 Å / Num. obs: 41097 / % possible obs: 92.85 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 10.93
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 2602 / CC1/2: 0.428

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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: 1.4→48.28 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.94
RfactorNum. reflection% reflection
Rfree0.181 1998 4.87 %
Rwork0.159 --
obs0.16 41054 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.91 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 0 298 1724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43450.2774820.29351607X-RAY DIFFRACTION54
1.4345-1.47330.30361130.27442181X-RAY DIFFRACTION73
1.4733-1.51670.26031360.2322684X-RAY DIFFRACTION90
1.5167-1.56560.23741470.2082881X-RAY DIFFRACTION96
1.5656-1.62160.22371490.18762904X-RAY DIFFRACTION97
1.6216-1.68650.19051490.182912X-RAY DIFFRACTION97
1.6865-1.76330.19931500.16742919X-RAY DIFFRACTION98
1.7633-1.85630.18971520.15722979X-RAY DIFFRACTION98
1.8563-1.97260.17081500.14322924X-RAY DIFFRACTION98
1.9726-2.12490.16171520.13932980X-RAY DIFFRACTION98
2.1249-2.33870.17431520.13932979X-RAY DIFFRACTION99
2.3387-2.67710.15351530.14562999X-RAY DIFFRACTION99
2.6771-3.37270.1761550.15413015X-RAY DIFFRACTION99
3.3727-48.2750.16881580.15023092X-RAY DIFFRACTION99
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)
11.08410.3084-0.05491.48010.18261.9269-0.01330.00160.00440.00440.00070.00360.0076-0.070.00030.08520-0.00670.0802-0.0020.0693104.8935-2.729422.4112
20.34350.31490.12260.33360.02910.19810.1082-0.1283-0.15380.2607-0.0809-0.10910.0303-0.20240.00070.20320.0236-0.01460.1411-0.02170.1718101.76724.581332.9026
31.4811-0.3028-0.07681.202-0.16871.47560.01950.0121-0.02310.00150.01080.0028-0.0079-0.01970.00140.06550.00130.00380.07140.00360.0966117.1061-5.58330.0319
40.113-0.13860.00070.2641-0.05530.17970.05950.0813-0.2239-0.1562-0.0914-0.16610.02060.0511-0.00130.16520.0056-0.00620.1328-0.0190.1924122.8121-13.6916-7.4626
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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