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- PDB-2iy1: SENP1 (mutant) full length SUMO1 -

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Basic information

Entry
Database: PDB / ID: 2iy1
TitleSENP1 (mutant) full length SUMO1
Components
  • SENTRIN-SPECIFIC PROTEASE 1
  • SMALL UBIQUITIN-RELATED MODIFIER 1
KeywordsHYDROLASE/NUCLEAR PROTEIN / HYDROLASE-NUCLEAR PROTEIN COMPLEX / NUCLEAR PROTEIN / UBL CONJUGATION PATHWAY / PROTEASE / HYDROLASE / UBIQUITIN / THIOL PROTEASE / PROTEIN PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / RHOF GTPase cycle / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / regulation of postsynapse assembly / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / transporter activator activity / nuclear pore / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of mRNA stability / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PML body / PKR-mediated signaling / regulation of protein stability / 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 / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear speck / nuclear body / focal adhesion / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily ...Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / 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 / 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 1 / Sentrin-specific protease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsShen, L. / Dong, C. / Naismith, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Sumo Protease Senp1 Induces Isomerization of the Scissile Peptide Bond.
Authors: Shen, L. / Tatham, M.H. / Dong, C. / Zagorska, A. / Naismith, J.H. / Hay, R.T.
History
DepositionJul 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 1
C: SENTRIN-SPECIFIC PROTEASE 1
D: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)73,0564
Polymers73,0564
Non-polymers00
Water2,036113
1
A: SENTRIN-SPECIFIC PROTEASE 1
B: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)36,5282
Polymers36,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SENTRIN-SPECIFIC PROTEASE 1
D: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)36,5282
Polymers36,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.232, 141.232, 98.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA421 - 6423 - 224
21PROPROLYSLYSCC421 - 6423 - 224
12ILEILESERSERBB17 - 943 - 80
22ILEILESERSERDD17 - 943 - 80

NCS ensembles :
ID
1
2

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Components

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


Mass: 26900.146 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 419-643 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein SMALL UBIQUITIN-RELATED MODIFIER 1 / SUMO-1 / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / ...SUMO-1 / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SENTRIN / SUMO1


Mass: 9627.966 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P63165
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 602 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 602 TO ALA

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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: 3.37 Å3/Da / Density % sol: 63.17 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: OSMIC MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.46→100 Å / Num. obs: 34278 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→40.72 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.248 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1810 5 %RANDOM
Rwork0.249 ---
obs0.251 34278 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.46→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 0 113 5239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9457032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12924.511266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.205151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0781530
X-RAY DIFFRACTIONr_chiral_restr0.10.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22294
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23553
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.53171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9624990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52232342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3734.52042
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1853tight positional0.070.05
2B631tight positional0.070.05
1A1853tight thermal0.130.5
2B631tight thermal0.10.5
LS refinement shellResolution: 2.46→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 125 -
Rwork0.298 2412 -
obs--94.91 %
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)
12.7208-0.25070.58472.3335-0.04183.9222-0.1071-0.0549-0.28450.0145-0.0275-0.0048-0.08120.18780.1346-0.2608-0.0870.051-0.1945-0.0258-0.083153.72944.27530.668
23.778-0.1356-2.31011.60550.78997.5617-0.24610.5796-0.5172-0.35860.0178-0.13570.09710.02250.2284-0.1995-0.06150.06050.0996-0.06450.150767.4138.2912.429
32.9554-0.68290.58092.2506-0.15542.99240.0483-0.0828-0.3536-0.0331-0.06260.05720.16190.08680.0143-0.2575-0.0060.0212-0.2332-0.0087-0.1401121.307113.50829.923
42.40650.2227-0.43732.06832.522417.8971-0.03290.4841-0.2283-0.19270.0752-0.3758-0.17930.9601-0.0423-0.21210.10460.05260.0706-0.05270.0694135.335110.86711.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 644
2X-RAY DIFFRACTION2B15 - 96
3X-RAY DIFFRACTION3C419 - 644
4X-RAY DIFFRACTION4D15 - 96

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