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

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Basic information

Entry
Database: PDB / ID: 4wjq
TitleCrystal Structure of SUMO1 in complex with Daxx
Components
  • Daxx
  • Small ubiquitin-related modifier 1
Keywordsprotein binding/signaling protein / SUMO1 / Daxx / Homo sapiens / SUMO Interaction Motif / PhosphoSIM / protein binding-signaling protein 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 / transporter activator activity / nuclear pore / 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 / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PML body / PKR-mediated signaling / regulation of protein stability / Formation of Incision Complex in GG-NER / protein tag activity / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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: 1.35 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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / 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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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)22,7354
Polymers22,7354
Non-polymers00
Water6,017334
1
A: Small ubiquitin-related modifier 1
B: Daxx


Theoretical massNumber of molelcules
Total (without water)11,3682
Polymers11,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area5820 Å2
MethodPISA
2
C: Small ubiquitin-related modifier 1
D: Daxx


Theoretical massNumber of molelcules
Total (without water)11,3682
Polymers11,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-3 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.637, 38.402, 73.691
Angle α, β, γ (deg.)90.000, 101.090, 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


Mass: 1840.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 26% PEG3350, 10 mM calcium chloride

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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 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 39759 / % possible obs: 94.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.52 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.1
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.4 / % possible all: 74.6

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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: 1.35→36.158 Å / FOM work R set: 0.8844 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2005 5.04 %Random selection
Rwork0.1558 37743 --
obs0.1571 39748 94.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.05 Å2 / Biso mean: 24.23 Å2 / Biso min: 8.37 Å2
Refinement stepCycle: final / Resolution: 1.35→36.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 334 1776
Biso mean---35.69 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091460
X-RAY DIFFRACTIONf_angle_d1.2351950
X-RAY DIFFRACTIONf_chiral_restr0.071213
X-RAY DIFFRACTIONf_plane_restr0.006253
X-RAY DIFFRACTIONf_dihedral_angle_d15.142572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.38380.31361020.27291903200566
1.3838-1.42120.23761250.24862243236881
1.4212-1.4630.22931320.21312649278194
1.463-1.51030.18691480.19632692284095
1.5103-1.56420.22611510.16972735288696
1.5642-1.62690.1981370.1632737287498
1.6269-1.70090.18831470.16682784293198
1.7009-1.79060.19651590.1632814297399
1.7906-1.90280.16491420.15912821296399
1.9028-2.04970.16421480.14732831297999
2.0497-2.25590.17021470.149528533000100
2.2559-2.58230.16731550.151328563011100
2.5823-3.2530.18511530.156228803033100
3.253-36.17070.17091590.136329453104100
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)
10.9394-0.54230.19551.6422-0.08060.5818-0.0097-0.0095-0.01130.03550.0295-0.0265-0.02030.05460.00020.0874-0.00520.00740.0946-0.01240.0974-0.2367-0.860532.0441
20.5067-0.4336-0.37250.41780.3620.32190.21780.0283-0.00750.00240.0685-0.05140.1865-0.26190.13690.1338-0.0334-0.02480.16940.00170.153-18.24514.214235.0498
30.05140.02240.00310.56880.7811.1049-0.07820.09580.235-0.2043-0.1531-0.0468-0.1018-0.0144-0.14720.1506-0.01340.03070.14120.03990.1667-4.68958.733826.0197
40.6422-0.2410.27670.95450.31820.74080.00190.0148-0.01110.0231-0.002-0.01660.0124-0.0342-00.10570.0004-0.00370.1046-0.00750.095-16.4087-5.69338.0756
50.2886-0.2387-0.03780.19330.01550.00840.03510.0591-0.0161-0.2325-0.07860.15770.0467-0.2552-0.06040.1612-0.0186-0.03030.1701-0.00750.1218-24.9153-12.98791.6166
60.11190.04740.03180.03240.01460.0078-0.06530.0021-0.02290.0531-0.070.00340.0893-0.0995-01.30820.2285-0.01210.93830.07290.8211-15.9776-15.79818.1254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:97 )A20 - 97
2X-RAY DIFFRACTION2( CHAIN B AND RESID 4:10 )B4 - 10
3X-RAY DIFFRACTION3( CHAIN B AND RESID 11:15 )B11 - 15
4X-RAY DIFFRACTION4( CHAIN C AND RESID 18:93 )C18 - 93
5X-RAY DIFFRACTION5( CHAIN D AND RESID 7:14 )D7 - 14
6X-RAY DIFFRACTION6( CHAIN D AND RESID 15:18 )D15 - 18

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