+Open data
-Basic information
Entry | Database: PDB / ID: 6x05 | |||||||||
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Title | Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4 | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Nucleoporin / Nanobody | |||||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / 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 ...mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / 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 / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation / nuclear pore / protein import into nucleus / double-strand break repair / nuclear envelope / cellular response to heat / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Vicugna pacos (alpaca) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Nordeen, S.A. / Schwartz, T.U. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif. Authors: Nordeen, S.A. / Turman, D.L. / 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 | 6x05.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x05.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 6x05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/6x05 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/6x05 | HTTPS FTP |
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-Related structure data
Related structure data | 6x02C 6x03C 6x04C 4q9tS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 48493.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NUP133, RAT3, YKR082W, YKR402 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: P36161 |
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#2: Antibody | Mass: 13505.921 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 24% PEG 3,350, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→59.57 Å / Num. obs: 39093 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 32.43 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.052 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3828 / CC1/2: 0.51 / Rpim(I) all: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q9T Resolution: 2.1→59.57 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1084 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→59.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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