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- PDB-2io3: Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2 -

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Basic information

Entry
Database: PDB / ID: 2io3
TitleCrystal structure of human Senp2 in complex with RanGAP1-SUMO-2
Components
  • Ran GTPase-activating protein 1
  • Sentrin-specific protease 2
  • Small ubiquitin-related modifier 2
KeywordsPROTEIN BINDING / HYDROLASE / SUMO / Ubiquitin / Senp / Ulp / complex
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / nuclear pore cytoplasmic filaments / SUMOylation of SUMOylation proteins / activation of GTPase activity / Rev-mediated nuclear export of HIV RNA / negative regulation of protein export from nucleus / SUMOylation of RNA binding proteins / nuclear export / regulation of Wnt signaling pathway / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / aggresome / fat cell differentiation / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / response to axon injury / mRNA transport / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / GTPase activator activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / hippocampal mossy fiber to CA3 synapse / positive regulation of protein ubiquitination / Regulation of endogenous retroelements by KRAB-ZFP proteins / GABA-ergic synapse / SUMOylation of intracellular receptors / RHO GTPases Activate Formins / protein destabilization / PML body / small GTPase binding / kinetochore / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / mitotic spindle / Separation of Sister Chromatids / nuclear envelope / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cadherin binding / intracellular membrane-bounded organelle / dendrite / ubiquitin protein ligase binding / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / 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 ...Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / 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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat / Papain-like cysteine peptidase superfamily / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Ubiquitin homologues / Alpha Horseshoe / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / Small ubiquitin-related modifier 2 / Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.
Authors: Reverter, D. / Lima, C.D.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 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
Revision 1.4Oct 20, 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THERE IS A DOMAIN-SWAPPED DIMER ACROSS CRYSTALLOGRAPHIC TWO-FOLD INVOLVING CHAIN C, FORMED BY SYMMETRY OPERATION 7555 (Y,X,1/3-Z)

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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
C: Ran GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)55,2793
Polymers55,2793
Non-polymers00
Water00
1
A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1

A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1

A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1

A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)221,11512
Polymers221,11512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Unit cell
Length a, b, c (Å)164.056, 164.056, 78.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Sentrin-specific protease 2 / Sentrin/SUMO-specific protease SENP2 / SMT3-specific isopeptidase 2 / Smt3ip2 / Axam2


Mass: 27342.648 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C548S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / Ubiquitin-like protein SMT3B / SMT3 homolog 2 / Sentrin-2 / HSMT3


Mass: 9265.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P61956
#3: Protein Ran GTPase-activating protein 1


Mass: 18670.543 Da / Num. of mol.: 1 / Fragment: c-terminal domain / Mutation: C573S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P46060

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 4000, 0.1M Lithium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 10581 / Num. obs: 10581 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.7 / % possible all: 97.3

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Phasing

Phasing MRRfactor: 0.49 / Cor.coef. Fo:Fc: 0.665
Highest resolutionLowest resolution
Rotation4 Å44.3 Å
Translation4 Å44.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 3.2→24.81 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 3583109.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.306 529 5.1 %RANDOM
Rwork0.277 ---
obs0.277 10451 98.1 %-
all-10451 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.190556 e/Å3
Displacement parametersBiso mean: 92.2 Å2
Baniso -1Baniso -2Baniso -3
1-23.31 Å229.46 Å20 Å2
2--23.31 Å20 Å2
3----46.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.2→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 0 3664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 92 5.4 %
Rwork0.366 1597 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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