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- PDB-2io1: Crystal structure of human Senp2 in complex with preSUMO-3 -

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Basic information

Entry
Database: PDB / ID: 2io1
TitleCrystal structure of human Senp2 in complex with preSUMO-3
Components
  • Sentrin-specific protease 2
  • Small ubiquitin-related modifier 3 precursor
KeywordsPROTEIN BINDING / HYDROLASE / SUMO / Ubiquitin / Senp / Ulp / complex
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / regulation of Wnt signaling pathway / fat cell differentiation ...SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / regulation of Wnt signaling pathway / fat cell differentiation / ubiquitin-like protein ligase binding / negative regulation of DNA binding / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of transcription factors / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / negative regulation of protein ubiquitination / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / protein destabilization / SUMOylation of intracellular receptors / kinetochore / PML body / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / protein transport / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) ...Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 3 / Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.
Authors: Reverter, D. / Lima, C.D.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 3 precursor
C: Sentrin-specific protease 2
D: Small ubiquitin-related modifier 3 precursor
E: Sentrin-specific protease 2
F: Small ubiquitin-related modifier 3 precursor


Theoretical massNumber of molelcules
Total (without water)113,7976
Polymers113,7976
Non-polymers00
Water5,008278
1
A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 3 precursor


Theoretical massNumber of molelcules
Total (without water)37,9322
Polymers37,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-3 kcal/mol
Surface area14480 Å2
MethodPISA
2
C: Sentrin-specific protease 2
D: Small ubiquitin-related modifier 3 precursor


Theoretical massNumber of molelcules
Total (without water)37,9322
Polymers37,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-0 kcal/mol
Surface area14820 Å2
MethodPISA
3
E: Sentrin-specific protease 2
F: Small ubiquitin-related modifier 3 precursor


Theoretical massNumber of molelcules
Total (without water)37,9322
Polymers37,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.980, 143.360, 134.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Details3 biological units in the asymmetric unit

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Components

#1: Protein Sentrin-specific protease 2 / Sentrin/SUMO-specific protease SENP2 / SMT3-specific isopeptidase 2 / Smt3ip2 / Axam2


Mass: 27342.648 Da / Num. of mol.: 3 / Fragment: catalytic domain / Mutation: C548S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier 3 precursor / SUMO-3 / Ubiquitin-like protein SMT3A / SMT3 homolog 1


Mass: 10589.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO3, SMT3A, SMT3H1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P55854
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 41896 / Num. obs: 40430 / % possible obs: 96.5 % / Observed criterion σ(I): -1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.102 / Χ2: 0.438 / Net I/σ(I): 4.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3093 / Χ2: 0.379 / % possible all: 75.1

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Phasing

Phasing MRRfactor: 0.381 / Cor.coef. Fo:Fc: 0.628
Highest resolutionLowest resolution
Rotation4 Å47.21 Å
Translation4 Å47.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.856 / Data cutoff high absF: 2619913 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1922 5 %RANDOM
Rwork0.204 ---
all-40430 --
obs-38679 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.785 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.68 Å20 Å20 Å2
2--2.8 Å20 Å2
3----9.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7538 0 0 278 7816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 217 4.7 %
Rwork0.3 4384 -
obs-4601 65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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