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Yorodumi- PDB-3uip: Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from... -
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-Basic information
Entry | Database: PDB / ID: 3uip | ||||||
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Title | Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II | ||||||
Components |
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Keywords | Ligase/Isomerase/Protein Binding / E3 / ligase / SUMO / UBC9 / RanBP2 / nuclear pore complex / Ligase-Isomerase-Protein Binding complex | ||||||
Function / homology | Function and homology information cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase activity / SUMO ligase complex / negative regulation of transcription by transcription factor localization / annulate lamellae / SUMOylation of nuclear envelope proteins ...cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase activity / SUMO ligase complex / negative regulation of transcription by transcription factor localization / annulate lamellae / SUMOylation of nuclear envelope proteins / transferase complex / 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) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / negative regulation of action potential / nuclear pore cytoplasmic filaments / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / SUMOylation of DNA methylation proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / activation of GTPase activity / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / aggresome / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / negative regulation of DNA binding / Vpr-mediated nuclear import of PICs / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / Signaling by ALK fusions and activated point mutants / response to axon injury / Regulation of HSF1-mediated heat shock response / potassium channel regulator activity / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / Mitotic Prometaphase / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / cellular response to cadmium ion / Resolution of Sister Chromatid Cohesion / response to amphetamine / Meiotic synapsis / GTPase activator activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / HCMV Late Events / chromosome segregation / RHO GTPases Activate Formins / transcription coregulator binding / positive regulation of protein-containing complex assembly / Transcriptional regulation by small RNAs / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / mitotic spindle / kinetochore Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å | ||||||
Authors | Gareau, J.R. / Reverter, D. / Lima, C.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. Authors: Gareau, J.R. / Reverter, D. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uip.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uip.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/3uip ftp://data.pdbj.org/pub/pdb/validation_reports/ui/3uip | HTTPS FTP |
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-Related structure data
Related structure data | 3uinC 3uioC 1z5sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18138.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC9, UBCE9, UBE2I / Plasmid details: 469008 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein | Mass: 9285.527 Da / Num. of mol.: 1 / Fragment: UNP residues 18-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Plasmid details: 469008 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165 |
#3: Protein | Mass: 18572.506 Da / Num. of mol.: 1 / Fragment: UNP residues 419-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1835, RANGAP1, SD / Plasmid details: 469008 / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46060 |
#4: Protein | Mass: 7803.704 Da / Num. of mol.: 1 / Fragment: UNP residues 2631-2695 / Mutation: A2642V, Q2644E, L2647K, T2649D, K2650T Source method: isolated from a genetically manipulated source Details: Motif II of RanBP2 IR1 was mutated to IR2 motif II. Source: (gene. exp.) Homo sapiens (human) / Gene: NUP358, RANBP2 / Plasmid details: 469008 / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49792 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.4 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG4000, 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.293→35 Å / Num. all: 39176 / Num. obs: 38980 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.293→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3840 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z5S Resolution: 2.293→33.978 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.951 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.7 Å2 / Biso mean: 38.8526 Å2 / Biso min: 15.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.293→33.978 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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