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- PDB-1kps: Structural Basis for E2-mediated SUMO conjugation revealed by a c... -
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Basic information
Entry | Database: PDB / ID: 1kps | ||||||
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Title | Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 | ||||||
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![]() | LIGASE/PROTEIN TRANSPORT / SUMO / UBIQUITIN / E2 / CONJUGATING ENZYME / LIGASE / THIOESTER / SMALL UBIQUITIN-LIKE MODIFIER / LIGASE-PROTEIN TRANSPORT COMPLEX | ||||||
Function / homology | ![]() SUMO E3 ligases SUMOylate target proteins / Postmitotic nuclear pore complex (NPC) reformation / small GTPase binding => GO:0031267 / SUMOylation of DNA replication proteins / cellular response to vasopressin / kinetochore => GO:0000776 / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding ...SUMO E3 ligases SUMOylate target proteins / Postmitotic nuclear pore complex (NPC) reformation / small GTPase binding => GO:0031267 / SUMOylation of DNA replication proteins / cellular response to vasopressin / kinetochore => GO:0000776 / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMO ligase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / RHO GTPases Activate Formins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Separation of Sister Chromatids / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / nuclear pore cytoplasmic filaments / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / negative regulation of protein export from nucleus / SUMOylation of RNA binding proteins / activation of GTPase activity / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / aggresome / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / cellular response to peptide hormone stimulus / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / response to axon injury / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / axon cytoplasm / Meiotic synapsis / SUMOylation of chromatin organization proteins / GTPase activator activity / SUMOylation of transcription cofactors / transcription coregulator binding / chromosome segregation / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / PML body / mitotic spindle / Formation of Incision Complex in GG-NER / 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 / nuclear membrane / positive regulation of cell migration / cell division / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / dendrite / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bernier-Villamor, V. / Sampson, D.A. / Matunis, M.J. / Lima, C.D. | ||||||
![]() | ![]() Title: Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. Authors: Bernier-Villamor, V. / Sampson, D.A. / Matunis, M.J. / Lima, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 118 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18117.893 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18615.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001 | |||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→19.25 Å / Num. all: 27248 / Num. obs: 27248 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.66 Å / Num. unique all: 4114 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 27902 / % possible obs: 96.2 % / Num. measured all: 274090 / Rmerge(I) obs: 0.08 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 92.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: 3 wavelength MAD dataset collected at NSLS beamline X4A to 2.8A Resolution: 2.5→19.25 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3260494.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.475 Å2 / ksol: 0.311999 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.3 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.4 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.393 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.357 |