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Yorodumi- PDB-3f3f: Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f3f | ||||||
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Title | Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Protein Complex / Nucleoporin / Nucleoporin Complex / Nuclear Pore Complex / Macromolecular Assembly / Membrane Coat / Nucleocytoplasmic Transport / beta-propeller / solenoid domain / mRNA transport / Nucleus / Protein transport / Translocation / WD repeat | ||||||
Function / homology | Function and homology information Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / structural constituent of nuclear pore / nucleocytoplasmic transport / vacuolar membrane / ribosomal large subunit export from nucleus / mRNA transport / mRNA export from nucleus ...Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / structural constituent of nuclear pore / nucleocytoplasmic transport / vacuolar membrane / ribosomal large subunit export from nucleus / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein import into nucleus / protein transport / nuclear envelope / nuclear membrane / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å | ||||||
Authors | Debler, E.W. / Hseo, H. / Ma, Y. / Blobel, G. / Hoelz, A. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: A fence-like coat for the nuclear pore membrane. Authors: Debler, E.W. / Ma, Y. / Seo, H.S. / Hsia, K.C. / Noriega, T.R. / 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 | 3f3f.cif.gz | 618.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f3f.ent.gz | 507.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/3f3f ftp://data.pdbj.org/pub/pdb/validation_reports/f3/3f3f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is the complete heterooctamer that is present in the asymmetric unit |
-Components
#1: Protein | Mass: 39406.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEH1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P53011 #2: Protein | Mass: 64929.242 Da / Num. of mol.: 4 / Fragment: UNP residues 1-570 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP85, RAT9 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P46673 |
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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: 3 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 10000, MES buffer, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2008 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 111202 / Num. obs: 108644 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.079 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 7406 / Rsym value: 0.079 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.9→50 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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