[English] 日本語
Yorodumi- PDB-3iko: Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iko | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN / PROTEIN TRANSPORT / NPC / TRANSPORT / WD REPEAT / AUTOCATALYTIC CLEAVAGE / MRNA TRANSPORT / NUCLEAR PORE COMPLEX / NUCLEUS / PHOSPHOPROTEIN / TRANSLOCATION / Coiled coil / Membrane / Hydrolase / RNA-binding / Cytoplasmic vesicle / Endoplasmic reticulum / ER-Golgi transport / NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / Seh1-associated complex / protein localization to nuclear inner membrane / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore central transport channel / regulation of TORC1 signaling / nuclear pore localization ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / protein localization to nuclear inner membrane / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore central transport channel / regulation of TORC1 signaling / nuclear pore localization / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / RNA export from nucleus / structural constituent of nuclear pore / vacuolar membrane / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / : / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / hydrolase activity / structural molecule activity / endoplasmic reticulum membrane / 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 / SAD / Resolution: 3.2 Å | ||||||
Authors | Nagy, V. / Hsia, K.-C. / Debler, E.W. / Davenport, A. / Blobel, G. / Hoelz, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Authors: Nagy, V. / Hsia, K.C. / Debler, E.W. / Kampmann, M. / Davenport, A.M. / Blobel, G. / Hoelz, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3iko.cif.gz | 617.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3iko.ent.gz | 506.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/3iko ftp://data.pdbj.org/pub/pdb/validation_reports/ik/3iko | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33082.965 Da / Num. of mol.: 3 / Fragment: UNP residues 1-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)-RIL / References: UniProt: Q04491 #2: Protein | Mass: 51013.898 Da / Num. of mol.: 3 / Fragment: UNP residues 731-1158 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUP145, RAT10, YGL092W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)-RIL References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #3: Protein | Mass: 52864.793 Da / Num. of mol.: 3 / Fragment: UNP residues 1-460 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-CODONPLUS (DE3)-RIL / References: UniProt: P52891 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.66 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.14 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 108829 / Num. obs: 105020 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.115 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.525 / % possible all: 75.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 3.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|