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Open data
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Basic information
Entry | Database: PDB / ID: 9gnn | ||||||
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Title | Structure of SENP5 in complex with SUMO2 | ||||||
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![]() | HYDROLASE / SUMO / cysteine protease / SENP family | ||||||
Function / homology | ![]() SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding ...SUMO-specific endopeptidase activity / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / PML body / kinetochore / Formation of Incision Complex in GG-NER / protein tag activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cell division / nucleolus / proteolysis / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reverter, D. / Li, Y. / Sanchez-Alba, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the human SENP5's SUMO isoform discrimination. Authors: Sanchez-Alba, L. / Ying, L. / Maletic, M.D. / De Bolos, A. / Borras-Gas, H. / Liu, B. / Varejao, N. / Amador, V. / Mulder, M.P.C. / Reverter, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 93.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.1 KB | Display | ![]() |
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Full document | ![]() | 471.9 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9gnvC ![]() 9gnxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24420.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96HI0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 9137.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: An AYE group is located at the C-terminus / Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→48.61 Å / Num. obs: 23655 / % possible obs: 90.1 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.36→2.51 Å / Num. unique obs: 1183 / CC1/2: 0.54 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Alphafold Resolution: 2.36→48.61 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.22 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.91 Å2 / Biso mean: 46.6879 Å2 / Biso min: 19.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→48.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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