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- PDB-2io0: Crystal structure of human Senp2 in complex with preSUMO-2 -

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Basic information

Entry
Database: PDB / ID: 2io0
TitleCrystal structure of human Senp2 in complex with preSUMO-2
Components
  • Sentrin-specific protease 2
  • Small ubiquitin-related modifier 2 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) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / regulation of Wnt signaling pathway / SUMOylation of RNA binding proteins ...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) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / regulation of Wnt signaling pathway / SUMOylation of RNA binding proteins / SUMO transferase activity / fat cell differentiation / ubiquitin-like protein ligase 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 / PML body / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Processing of DNA double-strand break ends / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / cytosol
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 2 / Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 2 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2305
Polymers37,9422
Non-polymers2883
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-39 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.204, 146.204, 104.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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.: 1 / 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 2 precursor / SUMO-2 / Ubiquitin-like protein SMT3B / SMT3 homolog 2 / Sentrin-2 / HSMT3


Mass: 10598.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P61956
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 4000, 0.2M Lithium sulfate, 0.1mM Tris-HCl, pH 8.0, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 18192 / Num. obs: 18192 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.042 / Χ2: 0.715 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1651 / Χ2: 0.299 / % possible all: 86.7

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Processing

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

1tgz


Resolution: 2.3→48.3 Å / Rfactor Rfree error: 0.008 / FOM work R set: 0.82 / Data cutoff high absF: 3134411.75 / 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
Rfree0.249 875 5.1 %RANDOM
Rwork0.207 ---
all-17291 --
obs-17291 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.425 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å22.12 Å20 Å2
2---2.89 Å20 Å2
3---5.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 15 129 2709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 141 5.8 %
Rwork0.312 2288 -
obs-2429 77 %
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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