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- PDB-3zo5: Structure of SENP2-Loop1 in complex with preSUMO-2 -

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Basic information

Entry
Database: PDB / ID: 3zo5
TitleStructure of SENP2-Loop1 in complex with preSUMO-2
Components
  • SENTRIN-SPECIFIC PROTEASE 2
  • SMALL UBIQUITIN-RELATED MODIFIER 2
KeywordsHYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN 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: 2.15 Å
AuthorsAlegre, K.O. / Reverter, D.
CitationJournal: Protein Sci. / Year: 2014
Title: Structural Insights Into the Senp6 Loop1 Structure in Complex with Sumo2.
Authors: Alegre, K.O. / Reverter, D.
History
DepositionFeb 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)38,1202
Polymers38,1202
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-1.2 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.518, 145.518, 104.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SENTRIN-SPECIFIC PROTEASE 2 / AXAM2 / SMT3-SPECIFIC ISOPEPTIDASE 2 / SMT3IP2 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP2 / SENP2 PROTEASE


Mass: 27797.127 Da / Num. of mol.: 1 / Fragment: RESIDUES 363-589 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: INSERTION OF PPPPAKGG INSTEAD OF F393 AND K394 FROM THE SENP2 NUMBERING
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HC62, Ulp1 peptidase
#2: Protein SMALL UBIQUITIN-RELATED MODIFIER 2 / SUMO-2 / HSMT3 / SMT3 HOMOLOG 2 / SUMO-3 / SENTRIN-2 / UBIQUITIN-LIKE PROTEIN SMT3A / SMT3A


Mass: 10322.604 Da / Num. of mol.: 1 / Fragment: RESIDUES 16-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61956
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINSERTION OF PPPPAKGG INSTEAD OF F393 AND K394 FROM THE SENP2 NUMBERING

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979494
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979494 Å / Relative weight: 1
ReflectionResolution: 2.15→48.33 Å / Num. obs: 23228 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 2.15→2.26 Å / Redundancy: 5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IO0

2io0


Resolution: 2.15→80.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.509 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSERTION OF PPPPAKGG INSTEAD OF F393 AND K394 FROM THE SENP2 NUMBERING
RfactorNum. reflection% reflectionSelection details
Rfree0.23627 1193 5.1 %RANDOM
Rwork0.18814 ---
obs0.19041 22034 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.15→80.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 0 45 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.9583518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7624.453128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56315492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7491515
X-RAY DIFFRACTIONr_chiral_restr0.1710.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.149→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 80 -
Rwork0.321 1527 -
obs--98.53 %

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