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Yorodumi- PDB-3pbp: Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleop... -
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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 | ||||||
Components |
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Keywords | 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 | Function and homology information nuclear pore linkers / : / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments ...nuclear pore linkers / : / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / structural constituent of nuclear pore / RNA export from nucleus / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus / ribosomal large 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 / molecular adaptor activity / RNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Debler, E.W. / Hoelz, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pbp.cif.gz | 477 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbp.ent.gz | 405.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbp ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP82, YJL061W, J1135, HRB187 / Production host: Escherichia coli (E. coli) / References: UniProt: P40368 #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.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP116, NSP116, YMR047C, YM9532.12C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02630 #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.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP159, NUP158, RAT7, YIL115C / Production host: Escherichia coli (E. coli) / References: UniProt: P40477 #4: Chemical | ChemComp-PGE / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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