+Open data
-Basic information
Entry | Database: PDB / ID: 3jro | ||||||
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Title | NUP84-NUP145C-SEC13 edge element of the NPC lattice | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / STRUCTURAL PROTEIN / PROTEIN COMPLEX / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / ER-GOLGI TRANSPORT / MEMBRANE / MRNA TRANSPORT / NUCLEAR PORE COMPLEX / NUCLEUS / PROTEIN TRANSPORT / TRANSLOCATION / TRANSPORT / WD REPEAT / AUTOCATALYTIC CLEAVAGE / HYDROLASE / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / regulation of TORC1 signaling / nuclear pore outer ring / telomere tethering at nuclear periphery / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein exit from endoplasmic reticulum / 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 / tRNA export from nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / subtelomeric heterochromatin formation / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4.004 Å | ||||||
Authors | Brohawn, S.G. / Schwartz, T.U. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice. Authors: Brohawn, S.G. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jro.cif.gz | 445.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jro.ent.gz | 382.3 KB | Display | PDB format |
PDBx/mmJSON format | 3jro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jro ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jro | 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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-Components
#1: Protein | Mass: 85364.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q04491, UniProt: P49687 |
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#2: Protein | Mass: 49248.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: P52891 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.22 Å3/Da / Density % sol: 70.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2008 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. all: 37090 / Num. obs: 37016 / % possible obs: 99.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 |
Reflection shell | Resolution: 4→4.14 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 4.004→49.887 Å / SU ML: -0 / σ(F): 1.89 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 134.876 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.004→49.887 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: CHAIN C |