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Yorodumi- PDB-1z5s: Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z5s | ||||||
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Title | Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 | ||||||
Components |
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Keywords | LIGASE / E3 / SUMO / UBC9 / NUCLEAR PORE 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 / annulate lamellae / negative regulation of transcription by transcription factor localization / 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 / annulate lamellae / negative regulation of transcription by transcription factor localization / 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 / nuclear pore cytoplasmic filaments / negative regulation of action potential / Vitamin D (calciferol) metabolism / synaptonemal complex / Nuclear Pore Complex (NPC) Disassembly / small protein activating enzyme binding / 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 SUMOylation proteins / SUMOylation of immune response proteins / Transport of Mature mRNA Derived from an Intronless Transcript / nuclear export / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / activation of GTPase activity / negative regulation of protein export from nucleus / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / 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 / nucleocytoplasmic transport / Maturation of nucleoprotein / 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 / SUMOylation of ubiquitinylation proteins / roof of mouth development / 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 / Regulation of HSF1-mediated heat shock response / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / cellular response to cadmium ion / response to amphetamine / Meiotic synapsis / SUMOylation of chromatin organization proteins / GTPase activator activity / 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 / ISG15 antiviral mechanism Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Reverter, D. / Lima, C.D. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Authors: Reverter, D. / Lima, C.D. | ||||||
History |
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Remark 999 | SEQUENCE COVALENT ISOPEPTIDE BOND BETWEEN RANGAP1 LYS524 AND SUMO C-TERMINUS GLY97. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z5s.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z5s.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z5s ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z5s | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 18030.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P63279, ubiquitin-protein ligase |
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#2: Protein | Mass: 9473.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBL1, SMT3C, SMT3H3 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P63165 |
#3: Protein | Mass: 18686.607 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1 / Plasmid: PSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P46060 |
#4: Protein | Mass: 9544.638 Da / Num. of mol.: 1 / Fragment: IR1-M domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Plasmid: PSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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: 3.81 Å3/Da / Density % sol: 67.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 24, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16464 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.1 / % possible all: 91.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RANGAP1-UBC9 COMPLEX Resolution: 3.01→29.69 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2281669.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 13.936 Å2 / ksol: 0.267286 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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