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- PDB-3pbp: Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pbp | ||||||
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Title | Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex | ||||||
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![]() | TRANSPORT PROTEIN / STRUCTURAL PROTEIN / beta-propeller / nucleoporin / mRNA export / mRNP remodelling / NUCLEOCYTOPLASMIC Transport / PROTEIN TRANSPORT / TRANSLOCATION / TRANSPORT / autoproteolysis / Fusion protein / PROTOONCOGENE / ONCOPROTEIN / Protein COMPLEX / Nucleus / Nuclear Envelope / Nuclear Pore Complex | ||||||
Function / homology | ![]() nuclear pore linkers / : / nuclear pore localization / adenyl-nucleotide exchange factor activity / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript ...nuclear pore linkers / : / nuclear pore localization / adenyl-nucleotide exchange factor activity / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / mRNA export from nucleus / nuclear pore / protein export from nucleus / protein import into nucleus / transcription corepressor activity / nuclear envelope / ATPase binding / nuclear membrane / RNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Debler, E.W. / Hoelz, A. | ||||||
![]() | ![]() Title: Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex. Authors: Yoshida, K. / Seo, H.S. / Debler, E.W. / Blobel, G. / Hoelz, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 477 KB | Display | ![]() |
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PDB format | ![]() | 405.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 534.4 KB | Display | ![]() |
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Full document | ![]() | 614.4 KB | Display | |
Data in XML | ![]() | 89 KB | Display | |
Data in CIF | ![]() | 119.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51982.461 Da / Num. of mol.: 4 / Fragment: N-terminal domain (NTD), UNP residues 1-452 / Mutation: C396S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NUP82, YJL061W, J1135, HRB187 / Production host: ![]() ![]() #2: Protein | Mass: 16832.180 Da / Num. of mol.: 4 / Fragment: C-terminal domain (CTD), UNP residues 967-1113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NUP116, NSP116, YMR047C, YM9532.12C / Production host: ![]() ![]() #3: Protein/peptide | Mass: 4167.491 Da / Num. of mol.: 4 / Fragment: Tail, UNP residues 1425-1460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NUP159, NUP158, RAT7, YIL115C / Production host: ![]() ![]() #4: Chemical | ChemComp-PGE / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2009 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 184127 / Num. obs: 181917 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rsym value: 0.097 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Num. unique all: 17910 / Rsym value: 0.473 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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