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- PDB-9gnv: Human SENP5 in complex with SUMO1 -

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Basic information

Entry
Database: PDB / ID: 9gnv
TitleHuman SENP5 in complex with SUMO1
Components
  • Sentrin-specific protease 5
  • Small ubiquitin-related modifier 1
KeywordsHYDROLASE / SENP / ULP / SUMO
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / protein localization to nuclear pore / : / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO-specific endopeptidase activity / protein localization to nuclear pore / : / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / 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 / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / 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 / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / Regulation of IFNG signaling / potassium channel regulator activity / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear speck / nuclear body / cell division / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
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 / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues ...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 / Small ubiquitin-related modifier 1, Ubl 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
Small ubiquitin-related modifier 1 / Sentrin-specific protease 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsReverter, D. / Sanchez-Alba, L. / Li, Y.
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 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sentrin-specific protease 5
B: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)33,6902
Polymers33,6902
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint1 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.062, 91.062, 146.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein Sentrin-specific protease 5 / Sentrin/SUMO-specific protease SENP5


Mass: 24420.264 Da / Num. of mol.: 1
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 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: 9269.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P63165
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.1 M Malic Ac., pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 9791 Å / Relative weight: 1
ReflectionResolution: 2.178→78.86 Å / Num. obs: 14291 / % possible obs: 94.2 % / Redundancy: 12.3 % / CC1/2: 0.996 / Net I/σ(I): 9.9
Reflection shellResolution: 2.178→2.328 Å / Num. unique obs: 715 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→78.86 Å / SU ML: 0.2517 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 695 4.86 %
Rwork0.1841 13595 -
obs0.1879 14290 73.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.01 Å2
Refinement stepCycle: LAST / Resolution: 2.18→78.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 63 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852247
X-RAY DIFFRACTIONf_angle_d0.95223021
X-RAY DIFFRACTIONf_chiral_restr0.0589326
X-RAY DIFFRACTIONf_plane_restr0.005386
X-RAY DIFFRACTIONf_dihedral_angle_d6.3784287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.350.3597370.2424819X-RAY DIFFRACTION22.6
2.35-2.580.3291960.23722015X-RAY DIFFRACTION55.36
2.58-2.960.30561660.22793123X-RAY DIFFRACTION85.76
2.96-3.720.26751780.18083715X-RAY DIFFRACTION100
3.72-78.860.22992180.16343923X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: 5.6292128087 Å / Origin y: -26.87706931 Å / Origin z: -5.5046033112 Å
111213212223313233
T0.162652199986 Å20.0011886612182 Å20.0434661967243 Å2-0.19312674888 Å2-0.02169565861 Å2--0.187287423769 Å2
L1.35588092924 °20.307768068864 °2-0.185706231027 °2-1.08182410466 °2-0.221637368797 °2--1.09549778669 °2
S-0.0688116791478 Å °0.107692290935 Å °-0.135535648921 Å °-0.0645640514371 Å °0.0268168842034 Å °-0.104151584379 Å °0.0396887665975 Å °0.00696478910887 Å °0.0182020302325 Å °
Refinement TLS groupSelection details: all

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