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- PDB-2iy0: SENP1 (mutant) SUMO1 RanGAP -

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Basic information

Entry
Database: PDB / ID: 2iy0
TitleSENP1 (mutant) SUMO1 RanGAP
Components
  • RAN GTPASE-ACTIVATING PROTEIN 1
  • SENTRIN-SPECIFIC PROTEASE 1
  • SMALL UBIQUITIN-RELATED MODIFIER 1
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX / HYDROLASE-ACTIVATOR COMPLEX / PROTEASE / HYDROLASE / UBIQUITIN / THIOL PROTEASE / LEUCINE- RICH REPEAT / UBL CONJUGATION PATHWAY / PROTEIN PROTEIN COMPLEX / GTPASE ACTIVATION / HYDROLASE-ACTIVATOR COMPLEX UBL CONJUGATION / NUCLEAR PROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / deSUMOylase activity / SUMOylation of nuclear envelope proteins ...regulation of definitive erythrocyte differentiation / SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / 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 / nuclear pore cytoplasmic filaments / small protein activating enzyme binding / activation of GTPase activity / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / Rev-mediated nuclear export of HIV RNA / Maturation of nucleoprotein / negative regulation of protein export from nucleus / nuclear export / SUMOylation of RNA binding proteins / RHOF GTPase cycle / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / aggresome / 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 / response to axon injury / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of mRNA stability / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / GTPase activator activity / SUMOylation of transcription cofactors / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / RHO GTPases Activate Formins / PML body / PKR-mediated signaling / regulation of protein stability / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / protein tag activity / mitotic spindle / Separation of Sister Chromatids / nuclear envelope / 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 / cadherin binding / focal adhesion / DNA repair / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / dendrite / ubiquitin protein ligase binding
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 / Small ubiquitin-related modifier 1, Ubl domain / Leucine rich repeat, ribonuclease inhibitor type / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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) / Alpha Horseshoe / Ubiquitin homologues / 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 1 / Sentrin-specific protease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 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 7, 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 1
B: SMALL UBIQUITIN-RELATED MODIFIER 1
C: RAN GTPASE-ACTIVATING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)53,5673
Polymers53,5673
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.380, 83.380, 148.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 26900.146 Da / Num. of mol.: 1 / 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: 9524.822 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) / References: UniProt: P63165
#3: Protein RAN GTPASE-ACTIVATING PROTEIN 1 / RANGAP


Mass: 17141.896 Da / Num. of mol.: 1 / Fragment: C-TERMINUS, RESIDUES 432-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46060
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, 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: 2.47 Å3/Da / Density % sol: 49.9 %

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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: 2.77→38 Å / Num. obs: 13161 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→37.35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 36.217 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.279 691 5 %RANDOM
Rwork0.228 ---
obs0.23 13161 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.77→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 0 6 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.965099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59724.602176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8615720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0611519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22600
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3171.52343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56623707
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.78431607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2694.51392
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: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 46 -
Rwork0.341 941 -
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)
15.24080.9072-0.92033.59260.41493.58120.0141-0.1334-0.05160.0591-0.2410.51090.1196-0.2660.2269-0.026-0.05840.0581-0.121-0.057-0.04787.303-27-12.867
212.0769-2.50613.90757.7839-1.96974.7567-0.20380.24871.6353-0.19610.09631.9103-0.7554-0.84720.10750.38170.2025-0.09270.2289-0.09470.9055-7.37-7.716-16.386
35.2171-2.97730.18856.4915-0.19492.8417-0.1783-0.29130.0331-0.12940.318-0.19430.1761-0.0658-0.13970.0042-0.0412-0.0128-0.0235-0.0572-0.114319.561-1.2759.714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 644
2X-RAY DIFFRACTION2B22 - 97
3X-RAY DIFFRACTION3C432 - 587

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