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- PDB-2g4d: Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1 -

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Basic information

Entry
Database: PDB / ID: 2g4d
TitleCrystal structure of human SENP1 mutant (C603S) in complex with SUMO-1
Components
  • SENP1 protein
  • Small ubiquitin-related modifier 1
KeywordsHydrolase/PROTEIN BINDING / protease / ubiquitin-like protein / SUMO maturation / SUMO deconjugation / Hydrolase-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / nuclear stress granule ...SUMO-specific endopeptidase activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / nuclear stress granule / protein desumoylation / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / RHOF GTPase cycle / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein ligase binding / negative regulation of DNA binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / regulation of mRNA stability / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nuclear body / protein stabilization / nuclear speck / DNA repair / focal adhesion / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / 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 / 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 / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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: 2.8 Å
AuthorsXu, Z. / Chau, S.F. / Lam, K.H. / Au, S.W.N.
Citation
Journal: Biochem.J. / Year: 2006
Title: Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease
Authors: Xu, Z. / Chau, S.F. / Lam, K.H. / Chan, H.Y. / Ng, T.B. / Au, S.W.N.
#1: Journal: Biochem.J. / Year: 2005
Title: Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
Authors: Xu, Z. / Au, S.W.N.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 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
Revision 1.4Nov 10, 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 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENP1 protein
B: Small ubiquitin-related modifier 1
C: SENP1 protein
D: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)66,9534
Polymers66,9534
Non-polymers00
Water97354
1
A: SENP1 protein
B: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)33,4772
Polymers33,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SENP1 protein
D: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)33,4772
Polymers33,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.308, 97.308, 102.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein SENP1 protein / / SENTRIN-specific protease 1


Mass: 24377.336 Da / Num. of mol.: 2 / Fragment: protease catalytic domain / Mutation: C603S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTWOE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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


Mass: 9099.363 Da / Num. of mol.: 2 / Fragment: residues 20-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63165
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.63 Å3/Da / Density % sol: 66.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.1M CAPS, 40% PEG400, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→57.166 Å / Num. all: 63395 / Num. obs: 23472 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.7
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 99.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.6 / Num. measured all: 9353 / Num. unique obs: 3444 / Rsym value: 0.491 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→57.1 Å / FOM work R set: 0.756 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1132 4.8 %RANDOM
Rwork0.248 ---
all0.248 23401 --
obs0.248 23401 98.9 %-
Solvent computationBsol: 44.421 Å2
Displacement parametersBiso mean: 45.519 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2---1.06 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 0 54 4716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 22
RfactorNum. reflection
Rfree0.366 42
Rwork0.367 1019
obs-1061
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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