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- PDB-3f3f: Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f3f | ||||||
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Title | Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 | ||||||
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![]() | 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 | ![]() Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins ...Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Debler, E.W. / Hseo, H. / Ma, Y. / Blobel, G. / Hoelz, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 618.1 KB | Display | ![]() |
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PDB format | ![]() | 507.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.8 KB | Display | ![]() |
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Full document | ![]() | 621.1 KB | Display | |
Data in XML | ![]() | 113.7 KB | Display | |
Data in CIF | ![]() | 153.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 |
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Components
#1: Protein | Mass: 39406.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SEH1 / Plasmid: pETDuet-1 / Production host: ![]() ![]() #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.) ![]() ![]() Gene: NUP85, RAT9 / Plasmid: pETDuet-1 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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