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- PDB-6nnq: Non-covalent structure of SENP1 in complex with SUMO2 -

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Basic information

Entry
Database: PDB / ID: 6nnq
TitleNon-covalent structure of SENP1 in complex with SUMO2
Components
  • Sentrin-specific protease 1
  • Small ubiquitin-related modifier 3
KeywordsHYDROLASE/PROTEIN BINDING / SUMOylation / SUMO2 / SENP1 / HYDROLASE-PROTEIN BINDING 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) / SUMOylation of immune response proteins / RHOF GTPase cycle / regulation of protein localization to nucleus / negative regulation of DNA binding ...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) / SUMOylation of immune response proteins / RHOF GTPase cycle / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / 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 / kinetochore / Formation of Incision Complex in GG-NER / protein tag activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / positive regulation of transcription by RNA polymerase II / proteolysis / 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 / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. ...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 / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 3 / Sentrin-specific protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.621 Å
AuthorsAmbaye, N.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Noncovalent structure of SENP1 in complex with SUMO2.
Authors: Ambaye, N.D.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 3


Theoretical massNumber of molelcules
Total (without water)35,5472
Polymers35,5472
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint3 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.732, 98.732, 101.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-733-

HOH

21A-738-

HOH

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Components

#1: Protein Sentrin-specific protease 1 / Sentrin/SUMO-specific protease SENP1


Mass: 26597.887 Da / Num. of mol.: 1 / Fragment: residues 421-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier 3 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 8949.065 Da / Num. of mol.: 1 / Fragment: residues 15-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO3, SMT3A, SMT3H1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55854
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6000, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→45.24 Å / Num. obs: 15667 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.997 / Net I/σ(I): 1.7
Reflection shellResolution: 2.62→2.74 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.621→33.354 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 775 4.95 %
Rwork0.229 --
obs0.2313 15656 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.621→33.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 48 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022543
X-RAY DIFFRACTIONf_angle_d0.5323418
X-RAY DIFFRACTIONf_dihedral_angle_d7.111547
X-RAY DIFFRACTIONf_chiral_restr0.041365
X-RAY DIFFRACTIONf_plane_restr0.003441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6213-2.78550.38131080.32832435X-RAY DIFFRACTION100
2.7855-3.00040.38811140.31862447X-RAY DIFFRACTION100
3.0004-3.30210.28731490.28012422X-RAY DIFFRACTION100
3.3021-3.77940.30911230.23242461X-RAY DIFFRACTION100
3.7794-4.75940.25031460.18192476X-RAY DIFFRACTION100
4.7594-33.3570.22631350.20032640X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.0889 Å / Origin y: 9.0123 Å / Origin z: 1.0509 Å
111213212223313233
T0.2289 Å20.0559 Å20.0722 Å2-0.3251 Å20.0122 Å2--0.47 Å2
L1.5608 °2-0.4092 °2-0.0406 °2-1.8359 °2-0.6101 °2--2.5582 °2
S0.0244 Å °0.0807 Å °0.27 Å °-0.1105 Å °-0.1701 Å °-0.2296 Å °-0.1568 Å °-0.1029 Å °0.1506 Å °
Refinement TLS groupSelection details: all

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