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- PDB-2ckh: SENP1-SUMO2 complex -

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Basic information

Entry
Database: PDB / ID: 2ckh
TitleSENP1-SUMO2 complex
Components
  • SENTRIN-SPECIFIC PROTEASE 1
  • SMALL UBIQUITIN-RELATED MODIFIER 2
KeywordsHYDROLASE / UBL CONJUGATION PATHWAY / NUCLEAR PROTEIN / PROTEASE CO- COMPLEX / SUMO / PROTEASE / THIOL PROTEASE
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / deSUMOylase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / RHOF GTPase cycle / SUMOylation of RNA binding proteins ...SUMO-specific endopeptidase activity / deSUMOylase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / RHOF GTPase cycle / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / regulation of mRNA stability / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / SUMOylation of intracellular receptors / PML body / protein tag activity / Formation of Incision Complex in GG-NER / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2 / Sentrin-specific protease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShen, L.N. / Dong, C. / Liu, H. / Hay, R.T. / Naismith, J.H.
CitationJournal: Biochem.J. / Year: 2006
Title: The Structure of Senp1-Sumo-2 Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing.
Authors: Shen, L.N. / Dong, C. / Liu, H. / Naismith, J.H. / Hay, R.T.
History
DepositionApr 18, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionApr 26, 2006ID: 2BZO
Revision 1.0Apr 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description
Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / refine / reflns / reflns_shell
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength / _diffrn_source.type / _refine.ls_R_factor_obs / _refine.pdbx_starting_model / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 1
B: SMALL UBIQUITIN-RELATED MODIFIER 2


Theoretical massNumber of molelcules
Total (without water)35,8662
Polymers35,8662
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.376, 143.376, 71.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SENTRIN-SPECIFIC PROTEASE 1 / SENTERIN PROTEASE 1 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP1


Mass: 26803.098 Da / Num. of mol.: 1 / Fragment: PROTEASE DOMAIN, RESIDUES 419-643
Source method: isolated from a genetically manipulated source
Details: COVALENTLY LINKED TO SUMO / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein SMALL UBIQUITIN-RELATED MODIFIER 2 / SUMO2 / SUMO-2 / UBIQUITIN-LIKE PROTEIN SMT3B / SMT3 HOMOLOG 2 / SENTRIN-2 / HSMT3


Mass: 9063.168 Da / Num. of mol.: 1
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
Compound detailsDEGRADES UBL1 AND SMT3H2 CONJUGATES AND RELEASES THE MONOMERS

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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: 6.06 Å3/Da / Density % sol: 79.54 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→120 Å / Num. obs: 13469 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 3.2→124.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 62.802 / SU ML: 0.439 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANY DISCREPANCY BETWEEN R-FACTORS CALCULATED BY SFCHECK AND/OR EDS MAY BE DUE TO THE USE OF TLS IN THE REFIMNEMENT OF THE STRUCTURE AS INDICATED ABOVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 716 5 %RANDOM
Rwork0.245 ---
obs0.249 13469 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.72 Å2
Baniso -1Baniso -2Baniso -3
1--11.71 Å2-5.85 Å20 Å2
2---11.71 Å20 Å2
3---17.56 Å2
Refinement stepCycle: LAST / Resolution: 3.2→124.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 0 0 2515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222568
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9423450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72824.478134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94615493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0251517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21741
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0480.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3071.51551
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.54222453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71231145
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1224.5997
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: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 53 -
Rwork0.35 1009 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.48791.1299-0.39157.2814-1.4032.9857-0.3462-0.6772-1.0110.48780.28950.72010.09540.04830.0567-0.08870.12810.0975-0.45920.0784-0.51567.7792-16.261418.2692
25.713-1.25184.27767.61391.54719.9295-0.22820.3173-0.6517-1.22390.0350.918-0.7802-0.20460.1931-0.3206-0.2657-0.1079-0.8029-0.03370.14154.2166-23.1027-1.5081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 643
2X-RAY DIFFRACTION2B14 - 92

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