[English] 日本語
![](img/lk-miru.gif)
- 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 | ||||||
![]() |
| ||||||
![]() | 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 | ![]() mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / 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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nagy, V. / Hsia, K.-C. / Debler, E.W. / Davenport, A. / Blobel, G. / Hoelz, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 617.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 506.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 544.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 772.3 KB | Display | |
Data in XML | ![]() | 136.9 KB | Display | |
Data in CIF | ![]() | 183.5 KB | Display | |
Arichive directory | ![]() ![]() | 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.) ![]() ![]() Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: ![]() ![]() #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.) ![]() ![]() Gene: NUP145, RAT10, YGL092W / Production host: ![]() ![]() 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.) ![]() ![]() Gene: NUP84, YDL116W / Production host: ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
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: ![]() ![]() ![]() |
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: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|