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- PDB-2xwu: CRYSTAL STRUCTURE OF IMPORTIN 13 - UBC9 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2xwu
TitleCRYSTAL STRUCTURE OF IMPORTIN 13 - UBC9 COMPLEX
Components
  • IMPORTIN13
  • SUMO-CONJUGATING ENZYME UBC9
KeywordsLIGASE/NUCLEAR PROTEIN / LIGASE-NUCLEAR PROTEIN COMPLEX / NUCLEAR IMPORT
Function / homology
Function and homology information


positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / transcription coregulator binding / chromosome segregation / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / PML body / small GTPase binding / Formation of Incision Complex in GG-NER / protein import into nucleus / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin 13 repeat 2 / Importin 13 repeat / Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain ...Importin 13 repeat 2 / Importin 13 repeat / Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Armadillo-like helical / Armadillo-type fold / Roll / Alpha Beta
Similarity search - Domain/homology
Importin-13 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGruenwald, M. / Bono, F.
CitationJournal: Embo J. / Year: 2011
Title: Structure of Importin13-Ubc9 Complex: Nuclear Import and Release of a Key Regulator of Sumoylation.
Authors: Gruenwald, M. / Bono, F.
History
DepositionNov 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-CONJUGATING ENZYME UBC9
B: IMPORTIN13


Theoretical massNumber of molelcules
Total (without water)126,3252
Polymers126,3252
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-8.3 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.700, 126.800, 184.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUMO-CONJUGATING ENZYME UBC9 / SUMO-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN 9 / UBIQUITIN CARRIER PROTEIN I / UBIQUITIN- ...SUMO-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN 9 / UBIQUITIN CARRIER PROTEIN I / UBIQUITIN-CONJUGATING ENZYME E2 I / UBIQUITIN-PROTEIN LIGASE I / P18 / UBC9


Mass: 18030.814 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: P63279, ubiquitin-protein ligase
#2: Protein IMPORTIN13 / IMP13 / KARYOPHERIN-13 / KAP13 / RAN-BINDING PROTEIN 13 / RANBP13


Mass: 108293.719 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: O94829
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.2 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 50 MM MES PH 6.5 25% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9997
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40287 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.49
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.37 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2X19 AND 1U9A

2x19

1u9a


Resolution: 2.8→45.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3441228.86 / Data cutoff low absF: 31.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2005 5 %RANDOM
Rwork0.226 ---
obs0.226 40230 99.4 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 62.8192 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--2.92 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8098 0 0 36 8134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.405
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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 shellHighest resolution: 2.8 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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