[English] 日本語
Yorodumi- PDB-5tvz: Solution NMR structure of Saccharomyces cerevisiae Pom152 Ig-like... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tvz | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution NMR structure of Saccharomyces cerevisiae Pom152 Ig-like repeat, residues 718-820 | |||||||||||||||||||||
Components | Nucleoporin POM152 | |||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / Nuclear Pore Complex / Ig-like fold / nuclear envelope membrane / cadherin like fold | |||||||||||||||||||||
Function / homology | Function and homology information nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery ...nuclear pore transmembrane ring / spindle pole body duplication / nuclear pore organization / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear envelope lumen / mRNA transport / nuclear pore / protein-membrane adaptor activity / nuclear periphery / cell periphery / protein import into nucleus / nuclear envelope / nuclear membrane / mitochondrion Similarity search - Function | |||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||||||||||||||
Authors | Dutta, K. / Sampathkumar, P. / Cowburn, D. / Almo, S.C. / Rout, M.P. / Fernandez-Martinez, J. | |||||||||||||||||||||
Funding support | United States, 6items
| |||||||||||||||||||||
Citation | Journal: Structure / Year: 2017 Title: Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Authors: Paula Upla / Seung Joong Kim / Parthasarathy Sampathkumar / Kaushik Dutta / Sean M Cahill / Ilan E Chemmama / Rosemary Williams / Jeffrey B Bonanno / William J Rice / David L Stokes / David ...Authors: Paula Upla / Seung Joong Kim / Parthasarathy Sampathkumar / Kaushik Dutta / Sean M Cahill / Ilan E Chemmama / Rosemary Williams / Jeffrey B Bonanno / William J Rice / David L Stokes / David Cowburn / Steven C Almo / Andrej Sali / Michael P Rout / Javier Fernandez-Martinez / Abstract: The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or ...The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals that the luminal domain is formed by a flexible string-of-pearls arrangement of nine repetitive cadherin-like Ig-like domains, indicating an evolutionary connection between NPCs and the cell adhesion machinery. The 16 copies of Pom152 known to be present in the yeast NPC are long enough to form the observed membrane ring, suggesting how interactions between Pom152 molecules help establish and maintain the NPC architecture. | |||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tvz.cif.gz | 635.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tvz.ent.gz | 526.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tvz_validation.pdf.gz | 475.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5tvz_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5tvz_validation.xml.gz | 125 KB | Display | |
Data in CIF | 5tvz_validation.cif.gz | 144.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/5tvz ftp://data.pdbj.org/pub/pdb/validation_reports/tv/5tvz | HTTPS FTP |
-Related structure data
Related structure data | 8543C C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 12741.649 Da / Num. of mol.: 1 / Fragment: UNP residues 718-820 Source method: isolated from a genetically manipulated source Details: Nuclear Pore Complex Assembly: Pore membrane protein (POM) Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POM152 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlusRIL / References: UniProt: P39685 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||
Sample conditions | Details: 10mM Hepes, 150mM NaCl, pH=6.8, 1mM DTT / Ionic strength: 160 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 2048 / Conformers submitted total number: 20 |