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Open data
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Basic information
Entry | Database: PDB / ID: 5t94 | |||||||||
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Title | Crystal structure of Kap60 bound to yeast RCC1 (Prp20) | |||||||||
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![]() | PROTEIN TRANSPORT / NUCLEAR PROTEIN / Nuclear Import / Importin alpha / RCC1 like Domain / RLD / NLS / PROTEIN TRANSPORT - NUCLEAR PROTEIN complex | |||||||||
Function / homology | ![]() proteasome localization / response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus ...proteasome localization / response to pheromone / Postmitotic nuclear pore complex (NPC) reformation / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nucleus organization / ribosomal subunit export from nucleus / guanyl-nucleotide exchange factor activity / protein import into nucleus / disordered domain specific binding / nuclear envelope / cell cycle / cell division / protein-containing complex binding / chromatin / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sankhala, R.S. / Lokareddy, R.K. / Pumroy, R.A. / Cingolani, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Three-dimensional context rather than NLS amino acid sequence determines importin alpha subtype specificity for RCC1. Authors: Sankhala, R.S. / Lokareddy, R.K. / Begum, S. / Pumroy, R.A. / Gillilan, R.E. / Cingolani, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362.8 KB | Display | ![]() |
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PDB format | ![]() | 297.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tbkC ![]() 3of7S ![]() 4pvzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Dimer as determined by Gel filtration chromatography and further verified using small angle x-ray scattering method. |
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Components
#1: Protein | Mass: 53082.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ran guanyl-nucleotide exchange factor Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pGEX-6P-1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 60499.043 Da / Num. of mol.: 1 / Mutation: T205A, D276E, K400R Source method: isolated from a genetically manipulated source Details: Yeast nuclear import adapter protein Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Plasmid: pET28a / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.52 % / Description: Large thick block |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na cacodylate, 0.1 M NaCl and 1.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Jul 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→15 Å / Num. obs: 33934 / % possible obs: 96 % / Redundancy: 4.7 % / Biso Wilson estimate: 72.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 49.9 |
Reflection shell | Resolution: 2.63→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.4 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PVZ and 3OF7 Resolution: 2.631→14.894 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.631→14.894 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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