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Yorodumi- PDB-5elj: Isoform-specific inhibition of SUMO-dependent protein-protein int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5elj | ||||||||||||
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Title | Isoform-specific inhibition of SUMO-dependent protein-protein interactions | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Ubiquitin / Sumoylation | ||||||||||||
Function / homology | Function and homology information 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) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...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) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of chromatin organization proteins / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / roof of mouth development / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / transcription factor binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / cellular response to cadmium ion / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / 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 / nuclear body / protein stabilization / 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 | ||||||||||||
Biological species | synthetic construct (others) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å | ||||||||||||
Authors | Hughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. ...Hughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Sci Signal / Year: 2017 Title: Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, ...Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5elj.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5elj.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 5elj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5elj_validation.pdf.gz | 405.7 KB | Display | wwPDB validaton report |
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Full document | 5elj_full_validation.pdf.gz | 405.6 KB | Display | |
Data in XML | 5elj_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 5elj_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/5elj ftp://data.pdbj.org/pub/pdb/validation_reports/el/5elj | HTTPS FTP |
-Related structure data
Related structure data | 5eluC 5eqlC 2uyzS 4n6tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13252.120 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Protein | Mass: 9686.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes sodium salt, 10% w/v polyethylene glycol 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: SAGITALLY FOCUSED Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→70.7 Å / Num. obs: 15526 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 13 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.2 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2UYZ and 4N6T Resolution: 1.983→54.001 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.983→54.001 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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