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- PDB-4wjn: Crystal structure of SUMO1 in complex with phosphorylated PML -

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Basic information

Entry
Database: PDB / ID: 4wjn
TitleCrystal structure of SUMO1 in complex with phosphorylated 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 / suppression of viral release by host / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / 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 / suppression of viral release by host / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / SUMO binding / small protein activating enzyme binding / negative regulation of action potential / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / myeloid cell differentiation / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / maintenance of protein location in nucleus / protein-containing complex localization / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / oncogene-induced cell senescence / branching involved in mammary gland duct morphogenesis / Regulation of RUNX1 Expression and Activity / positive regulation of extrinsic apoptotic signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / cobalt ion binding / 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 / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / transcription factor binding / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / positive regulation of signal transduction by p53 class mediator / postsynaptic cytosol / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of ubiquitin-dependent protein catabolic process / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / protein targeting / regulation of cell adhesion / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / response to UV / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / positive regulation of defense response to virus by host / Transcriptional and post-translational regulation of MITF-M expression and activity / response to cytokine / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN localization / DNA damage response, signal transduction by p53 class mediator / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / response to gamma radiation / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of cell growth / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER
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: 1.5 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)12,8242
Polymers12,8242
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.274, 47.079, 63.986
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: 3296.901 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.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium cacodylate, 16% PEG3350, 10mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 14, 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: 1.5→37.921 Å / Num. all: 18558 / Num. obs: 18507 / % possible obs: 96.71 % / Redundancy: 9.8 % / Biso Wilson estimate: 14.54 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.1 / % possible all: 81.8

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Processing

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

2uyz


Resolution: 1.5→37.921 Å / FOM work R set: 0.8852 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 926 5 %Random selection
Rwork0.1583 17581 --
obs0.16 18507 96.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.2 Å2 / Biso mean: 22.51 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.5→37.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 0 146 922
Biso mean---37.86 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01792
X-RAY DIFFRACTIONf_angle_d1.2981063
X-RAY DIFFRACTIONf_chiral_restr0.05113
X-RAY DIFFRACTIONf_plane_restr0.007135
X-RAY DIFFRACTIONf_dihedral_angle_d16.126314
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 (%)
1.5-1.57910.23021080.22822046215480
1.5791-1.6780.19841300.18742452258297
1.678-1.80760.21621340.161425632697100
1.8076-1.98950.231350.166125732708100
1.9895-2.27740.20241370.149925862723100
2.2774-2.86910.1911370.156726172754100
2.8691-37.93270.17021450.148327442889100
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)
11.7170.2104-0.00481.7897-0.00441.43980.03380.0354-0.0399-0.0606-0.05340.02080.03750.01460.00420.090.0049-0.00490.0831-0.00730.0969-0.89377.363-6.8344
23.6242-0.0627-0.29584.95062.18455.0930.07230.0832-0.0777-0.26190.0363-0.2853-0.0950.12520.00330.0966-0.00250.01140.1285-0.00740.13528.240913.0807-8.675
32.30460.6987-1.31983.2331-0.78556.833-0.08110.0751-0.25850.0280.08930.7417-0.0199-0.315-0.08050.2659-00.00720.2808-0.04370.308829.9738-4.1336-15.5926
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 7:14 OR RESID 15:17 ) )B7 - 14
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 7:14 OR RESID 15:17 ) )B15 - 17
4X-RAY DIFFRACTION3( CHAIN B AND RESID 24:29 )B24 - 29

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