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- PDB-4wjp: Crystal Structure of SUMO1 in complex with phosphorylated Daxx -

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Basic information

Entry
Database: PDB / ID: 4wjp
TitleCrystal Structure of SUMO1 in complex with phosphorylated Daxx
Components
  • DaxxDeath-associated protein 6
  • Small ubiquitin-related modifier 1
Keywordsprotein binding/signaling protein / SUMO1 / Daxx / SUMO Interaction Motif / PhosphoSIM / protein binding-signaling protein complex
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 SUMOylation proteins / SUMOylation of immune response 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 / SUMOylation of ubiquitinylation proteins / roof of mouth development / 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 / nuclear pore / Regulation of IFNG signaling / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
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
AuthorsCappadocia, L. / Mascle, X.H. / Bourdeau, V. / Tremblay-Belzile, S. / Chaker-Margot, M. / Lussier-Price, M. / Wada, J. / Sakaguchi, K. / Aubry, M. / Ferbeyre, G. / Omichinski, J.G.
CitationJournal: Structure / Year: 2015
Title: Structural and Functional Characterization of the Phosphorylation-Dependent Interaction between PML and SUMO1.
Authors: Cappadocia, L. / Mascle, X.H. / Bourdeau, V. / Tremblay-Belzile, S. / Chaker-Margot, M. / Lussier-Price, M. / Wada, J. / Sakaguchi, K. / Aubry, M. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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: Daxx
C: Small ubiquitin-related modifier 1
D: Daxx


Theoretical massNumber of molelcules
Total (without water)23,0554
Polymers23,0554
Non-polymers00
Water3,189177
1
A: Small ubiquitin-related modifier 1
B: Daxx


Theoretical massNumber of molelcules
Total (without water)11,5282
Polymers11,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Small ubiquitin-related modifier 1
D: Daxx


Theoretical massNumber of molelcules
Total (without water)11,5282
Polymers11,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.266, 38.069, 73.950
Angle α, β, γ (deg.)90.000, 101.040, 90.000
Int Tables number4
Space group name H-MP1211

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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: 9526.771 Da / Num. of mol.: 2 / Fragment: unp residues 17-97 / 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 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P63165
#2: Protein/peptide Daxx / Death-associated protein 6


Mass: 2000.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM sodium cacodylate, 26% PEG3350, 10mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 20835 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
XDSdata scaling
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHENIXphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1555)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UYZ

2uyz


Resolution: 1.7→33.713 Å / FOM work R set: 0.8575 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1051 5.05 %Random selection
Rwork0.1628 19770 --
obs0.1645 20821 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.72 Å2 / Biso mean: 34.91 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 1.7→33.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 0 177 1642
Biso mean---42.33 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121496
X-RAY DIFFRACTIONf_angle_d1.2532007
X-RAY DIFFRACTIONf_chiral_restr0.055216
X-RAY DIFFRACTIONf_plane_restr0.006260
X-RAY DIFFRACTIONf_dihedral_angle_d16.926592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.77740.29421290.252524332562
1.7774-1.87110.21681330.206724282561
1.8711-1.98830.22311230.184624852608
1.9883-2.14180.19391350.173724642599
2.1418-2.35730.2031340.165624362570
2.3573-2.69830.20621310.169525042635
2.6983-3.3990.20131310.169224792610
3.399-33.71970.16511350.13525412676
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)
12.393-0.6240.5233.76750.1862.40780.03830.1220.0358-0.0556-0.0675-0.08460.01350.10790.04850.1195-0.00270.00890.1336-0.00790.1682-0.4062-0.976131.9142
26.42921.42810.35024.1568-0.25863.83280.48560.0371-0.31860.0324-0.1729-0.05040.4696-0.6389-0.38620.2751-0.0351-0.01880.1876-0.00260.2725-17.19874.657733.4392
34.7896-0.74032.22784.97921.94782.8782-0.25720.45880.7236-0.4607-0.1457-0.8832-0.72720.53160.38920.253-0.05890.05340.23320.06460.376-3.58839.601926.1435
42.1707-0.38240.54433.08321.01222.61010.0186-0.01770.00710.01660.0087-0.01420.1023-0.1181-0.01860.19690.0033-0.01560.2095-0.00270.153-15.7812-5.91017.95
55.1161-0.65991.11155.81370.45649.73980.03140.3757-0.5656-0.4561-0.18190.3395-0.3165-0.46520.54210.34120.0083-0.02330.41720.02180.3131-24.7415-13.1961.7673
62.1-0.48952.78360.1264-0.68373.78840.1777-0.18840.1903-0.191-0.217-0.0593-0.1633-0.12010.06771.0735-0.0717-0.19011.57260.58180.9082-16.5052-17.113918.6843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:97 )A19 - 97
2X-RAY DIFFRACTION2( CHAIN B AND RESID 6:10 )B6 - 10
3X-RAY DIFFRACTION3( CHAIN B AND ( RESID 11:14 OR RESID 15:15 ) )B11 - 14
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 11:14 OR RESID 15:15 ) )B15
5X-RAY DIFFRACTION4( CHAIN C AND RESID 18:94 )C18 - 94
6X-RAY DIFFRACTION5( CHAIN D AND RESID 7:14 )D7 - 14
7X-RAY DIFFRACTION6( CHAIN D AND RESID 15:18 )D15 - 18

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