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- PDB-9gnn: Structure of SENP5 in complex with SUMO2 -

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Basic information

Entry
Database: PDB / ID: 9gnn
TitleStructure of SENP5 in complex with SUMO2
Components
  • Sentrin-specific protease 5
  • Small ubiquitin-related modifier 3
KeywordsHYDROLASE / SUMO / cysteine protease / SENP family
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / negative regulation of DNA binding / 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 / SUMOylation of transcription factors ...SUMO-specific endopeptidase activity / negative regulation of DNA binding / 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 / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / 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
Sentrin-specific protease 3/5, conserved domain / Sentrin-specific protease 3/5 N-terminal / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. ...Sentrin-specific protease 3/5, conserved domain / Sentrin-specific protease 3/5 N-terminal / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Small ubiquitin-related modifier 3 / Sentrin-specific protease 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsReverter, D. / Li, Y. / Sanchez-Alba, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2025
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
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sentrin-specific protease 5
B: Sentrin-specific protease 5
C: Small ubiquitin-related modifier 3
D: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2296
Polymers67,1154
Non-polymers1142
Water43224
1
A: Sentrin-specific protease 5
C: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,5582
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sentrin-specific protease 5
D: Small ubiquitin-related modifier 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,5582
Non-polymers571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.162, 87.902, 116.676
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 Sentrin-specific protease 5 / Sentrin/SUMO-specific protease SENP5


Mass: 24420.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP5, FKSG45 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96HI0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier 3 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3A / Smt3A


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.) Homo sapiens (human) / Gene: SUMO3, SMT3A, SMT3H1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55854
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.36→2.51 Å / Num. unique obs: 1183 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
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
RfactorNum. reflection% reflection
Rfree0.2826 1161 4.94 %
Rwork0.213 22330 -
obs0.2165 23491 82.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.91 Å2 / Biso mean: 46.6879 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2.36→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 8 24 4428
Biso mean--37.95 40.63 -
Num. residues----534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.470.4298290.373856659517
2.47-2.60.4491040.33172184228865
2.6-2.760.38711490.30622979312888
2.76-2.970.32381840.282133433527100
2.97-3.270.36731610.271833973558100
3.27-3.750.29751830.21172992317589
3.75-4.720.2411650.17073287345295
4.72-48.610.22651860.173235823768100

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