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- PDB-6uyx: Crystal structure of K37-acetylated SUMO1 in complex with phospho... -

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Basic information

Entry
Database: PDB / ID: 6uyx
TitleCrystal structure of K37-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 / SUMOylation of SUMOylation proteins / XY body / 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 / : / 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: 1.7 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 / refine / refine_hist / refine_ls_restr_ncs / refine_ls_shell / struct_asym / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / 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.occupancy / _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_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_restr_ncs.pdbx_rms / _refine_ls_restr_ncs.pdbx_type / _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 / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.selection_details
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 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

Downloads & links

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Assembly

Deposited unit
C: Small ubiquitin-related modifier 1
D: phosphorylated DAXX
A: Small ubiquitin-related modifier 1
B: phosphorylated DAXX


Theoretical massNumber of molelcules
Total (without water)23,1374
Polymers23,1374
Non-polymers00
Water2,450136
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 area930 Å2
ΔGint-3 kcal/mol
Surface area5760 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 area1120 Å2
ΔGint-4 kcal/mol
Surface area5550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.292, 81.452, 34.284
Angle α, β, γ (deg.)90.00, 112.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211(CHAIN C AND RESID 19 THROUGH 95)
112(CHAIN B AND RESID 7 THROUGH 15)
212CHAIN D

NCS ensembles :
ID
1
2

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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.: 136 / 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: 1.91 Å3/Da / Density % sol: 35.71 %
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: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 S 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
Reflection twinOperator: l,-k,h / Fraction: 0.5
ReflectionResolution: 1.7→31.694 Å / Num. obs: 18373 / % possible obs: 95.83 % / Redundancy: 3.3 % / CC1/2: 0.996 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 1554 / CC1/2: 0.269

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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: 1.7→31.69 Å / Cross valid method: THROUGHOUT / σ(F): 58.61 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.21 1835 10.3 %
Rwork0.159 --
obs0.169 18373 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 0 136 1570
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A765X-RAY DIFFRACTIONPOSITIONAL
12C765X-RAY DIFFRACTIONPOSITIONAL
21B0X-RAY DIFFRACTIONPOSITIONAL
22D0X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.74620.42271200.32941052X-RAY DIFFRACTION72
1.7462-1.79760.35431330.32121220X-RAY DIFFRACTION83
1.7976-1.85560.31361410.28621239X-RAY DIFFRACTION86
1.8556-1.92190.26851450.24171302X-RAY DIFFRACTION87
1.9219-1.99890.24361390.22371278X-RAY DIFFRACTION87
1.9989-2.08980.2471400.20591254X-RAY DIFFRACTION88
2.0898-2.20.21011430.19491311X-RAY DIFFRACTION88
2.2-2.33780.23511430.1841286X-RAY DIFFRACTION88
2.3378-2.51820.19841500.17081299X-RAY DIFFRACTION88
2.5182-2.77150.21541410.17211297X-RAY DIFFRACTION88
2.7715-3.17220.23081470.14841334X-RAY DIFFRACTION89
3.1722-3.99540.18841500.1321313X-RAY DIFFRACTION89
3.9954-31.6940.18221420.1131343X-RAY DIFFRACTION90
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)
11.33470.77690.55881.13310.13141.20610.00890.0027-0.04570.0193-0.0062-0.01330.02920.01580.00050.1853-0.0115-0.02210.1527-0.00580.189925.277-11.417214.3394
20.1460.0508-0.15560.20460.1270.33510.06610.1388-0.16740.01290.0422-0.0843-0.10330.19720.01010.18940.0045-0.07020.1715-0.0170.201135.8105-7.304517.4531
30.97060.25190.16251.1434-0.92211.5677-0.0024-0.04870.01340.0486-0.00050.0372-0.0603-0.039-0.00030.20460.006-0.01280.16550.01520.154814.45144.4335-1.343
40.2254-0.18770.11110.2057-0.14190.26090.03-0.04320.05850.4284-0.2099-0.0189-0.207-0.2350.0030.2712-0.0014-0.04240.18510.00960.247412.8882-1.18539.9059
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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