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- PDB-2io2: Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 -

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Basic information

Entry
Database: PDB / ID: 2io2
TitleCrystal structure of human Senp2 in complex with RanGAP1-SUMO-1
Components
  • Ran GTPase-activating protein 1
  • Sentrin-specific protease 2
  • Small ubiquitin-related modifier 1
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 / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity ...SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / 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) / protein desumoylation / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear pore cytoplasmic filaments / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / nuclear export / Maturation of nucleoprotein / Rev-mediated nuclear export of HIV RNA / activation of GTPase activity / negative regulation of protein export from nucleus / SUMOylation of RNA binding proteins / aggresome / regulation of Wnt signaling pathway / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / fat cell differentiation / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / mRNA transport / response to axon injury / potassium channel regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / GTPase activator activity / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / RHO GTPases Activate Formins / positive regulation of protein-containing complex assembly / protein destabilization / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / mitotic spindle / protein tag activity / kinetochore / small GTPase binding / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Separation of Sister Chromatids / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear envelope / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear body / nuclear speck / cadherin binding / DNA repair / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / signal transduction / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
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 / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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 / 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 / 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) / Ubiquitin homologues / Ubiquitin-like domain / Alpha Horseshoe / Ubiquitin domain profile. / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 1
C: Ran GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)55,4873
Polymers55,4873
Non-polymers00
Water1448
1
A: Sentrin-specific protease 2
B: Small ubiquitin-related modifier 1
C: Ran GTPase-activating protein 1

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

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

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


Theoretical massNumber of molelcules
Total (without water)221,94812
Polymers221,94812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area37350 Å2
ΔGint-210 kcal/mol
Surface area75900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)163.960, 163.960, 77.770
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 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: 9473.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P63165
#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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
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: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 14174 / Num. obs: 13707 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Rmerge(I) obs: 0.071 / Χ2: 1.572 / Net I/σ(I): 25.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1260 / Χ2: 0.691 / % possible all: 91.2

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Phasing

Phasing MRRfactor: 0.518 / Cor.coef. Fo:Fc: 0.376
Highest resolutionLowest resolution
Rotation4 Å43.96 Å
Translation4 Å43.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 2.9→14.94 Å / Rfactor Rfree error: 0.012 / FOM work R set: 0.671 / Data cutoff high absF: 3563397 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.301 676 5 %RANDOM
Rwork0.268 ---
all-13579 --
obs-13579 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.216 e/Å3
Displacement parametersBiso mean: 90.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.04 Å214.98 Å20 Å2
2--10.04 Å20 Å2
3----20.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å1.12 Å
Refinement stepCycle: LAST / Resolution: 2.9→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 0 8 3696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it2.431.5
X-RAY DIFFRACTIONc_mcangle_it4.212
X-RAY DIFFRACTIONc_scbond_it3.482
X-RAY DIFFRACTIONc_scangle_it5.512.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 102 4.9 %
Rwork0.438 2001 -
obs-2103 92.7 %
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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