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- PDB-4wjo: Crystal Structure of SUMO1 in complex with PML -

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Basic information

Entry
Database: PDB / ID: 4wjo
TitleCrystal Structure of SUMO1 in complex with PML
Components
  • Protein PML
  • Small ubiquitin-related modifier 1
Keywordsprotein binding/signaling protein / SUMO1 / PML / SUMO Interaction Motif / PhosphoSIM / protein binding-signaling protein complex
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / suppression of viral release by host / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / suppression of viral release by host / protein localization to nuclear pore / 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) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / small protein activating enzyme binding / SUMO binding / positive regulation of apoptotic process involved in mammary gland involution / : / fibroblast migration / regulation of calcium ion transmembrane transport / endoplasmic reticulum calcium ion homeostasis / SMAD protein signal transduction / positive regulation of telomere maintenance / SUMOylation of DNA methylation proteins / myeloid cell differentiation / regulation of double-strand break repair / maintenance of protein location in nucleus / SUMOylation of immune response proteins / XY body / protein-containing complex localization / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of extrinsic apoptotic signaling pathway / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / 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 / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / transcription factor binding / entrainment of circadian clock by photoperiod / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of signal transduction by p53 class mediator / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of mitotic cell cycle / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein targeting / cellular response to interleukin-4 / regulation of cell adhesion / potassium channel regulator activity / retinoic acid receptor signaling pathway / positive regulation of defense response to virus by host / negative regulation of ubiquitin-dependent protein catabolic process / nuclear pore / Regulation of IFNG signaling / SUMOylation of DNA damage response and repair proteins / response to UV / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to cadmium ion / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / response to cytokine / SUMOylation of transcription cofactors / response to gamma radiation / cellular response to leukemia inhibitory factor / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / PKR-mediated signaling / PML body / negative regulation of cell growth / nuclear matrix / Formation of Incision Complex in GG-NER / HCMV Early Events
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / : / ANCHR-like B-box zinc-binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
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: 1.46 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_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_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: Protein PML


Theoretical massNumber of molelcules
Total (without water)12,5042
Polymers12,5042
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.388, 47.253, 63.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 9526.771 Da / Num. of mol.: 1 / Fragment: SUMO1, 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 Protein PML / Promyelocytic leukemia protein / RING finger protein 71 / Tripartite motif-containing protein 19


Mass: 2976.985 Da / Num. of mol.: 1 / Fragment: PML, unp residues 547-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P29590
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium cacodylate pH6.5, 16% PEG3350, 10mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 20770 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.96 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.6
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

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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: 1.46→26.47 Å / FOM work R set: 0.8933 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 1037 5 %Random selection
Rwork0.1566 19683 --
obs0.158 20720 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.03 Å2 / Biso mean: 21.56 Å2 / Biso min: 8.82 Å2
Refinement stepCycle: final / Resolution: 1.46→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 148 900
Biso mean---36.15 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01761
X-RAY DIFFRACTIONf_angle_d1.3631016
X-RAY DIFFRACTIONf_chiral_restr0.08110
X-RAY DIFFRACTIONf_plane_restr0.006132
X-RAY DIFFRACTIONf_dihedral_angle_d14.97298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4577-1.53460.22931390.21612644278394
1.5346-1.63070.1791460.170927662912100
1.6307-1.75660.19331470.159227982945100
1.7566-1.93330.16551480.157828052953100
1.9333-2.2130.16341490.145928292978100
2.213-2.78760.17911510.154528663017100
2.7876-26.47420.19411570.152829753132100
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)
11.1592-0.1020.37981.21310.29330.58760.0466-0.04-0.0607-0.0037-0.04440.00150.02640.0295-0.00250.09840.0018-0.00110.0967-0.00070.0975-0.91887.3458-6.7601
20.0426-0.03010.00940.1-0.07660.29070.0648-0.2679-0.01620.1121-0.0052-0.121-0.16690.1011-0.00350.1241-0.0076-0.00550.1573-0.01210.12386.724317.0659-5.2075
30.06870.0658-0.03070.12220.00990.044-0.0613-0.0010.04620.04070.01910.4133-0.0787-0.17940.00130.2075-0.0150.03420.2037-0.02770.220829.9626-4.3277-15.4515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:94 )A18 - 94
2X-RAY DIFFRACTION2( CHAIN B AND RESID 7:15 )B7 - 15
3X-RAY DIFFRACTION3( CHAIN B AND RESID 24:29 )B24 - 29

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