+Open data
-Basic information
Entry | Database: PDB / ID: 3fwb | ||||||
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Title | Sac3:Sus1:Cdc31 complex | ||||||
Components |
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Keywords | cell cycle / transcription / gene gating / complex / Cell division / Mitosis / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport / Transcription regulation | ||||||
Function / homology | Function and homology information half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / Golgi vesicle transport / mitotic spindle pole body / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ...half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / Golgi vesicle transport / mitotic spindle pole body / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / mRNA 3'-end processing / SAGA complex / poly(A)+ mRNA export from nucleus / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / nuclear pore / enzyme activator activity / protein export from nucleus / transcription elongation by RNA polymerase II / P-body / microtubule cytoskeleton organization / nuclear envelope / regulation of protein localization / protein transport / chromatin organization / mitotic cell cycle / ribosomal small subunit biogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / molecular adaptor activity / cell division / chromatin binding / calcium ion binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Stewart, M. / Jani, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export. Authors: Jani, D. / Lutz, S. / Marshall, N.J. / Fischer, T. / Kohler, A. / Ellisdon, A.M. / Hurt, E. / Stewart, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fwb.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fwb.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3fwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fwb_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 3fwb_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 3fwb_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3fwb_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/3fwb ftp://data.pdbj.org/pub/pdb/validation_reports/fw/3fwb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Sac3:Cdc31:Sus1 component of TREX-2 complex |
-Components
#1: Protein | Mass: 18774.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: see publication for complete details Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC31, DSK1, YOR257W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06704 |
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#2: Protein | Mass: 6767.702 Da / Num. of mol.: 1 / Fragment: residues 752-805 Source method: isolated from a genetically manipulated source Details: see publication for complete details Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LEP1, SAC3, YD8358.13, YDR159W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46674 |
#3: Protein | Mass: 11094.497 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: see publication for complete details Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUS1, YBR111W-A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WNK7 |
#4: 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: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH6.5, 16% PEG4K, 20% glycerol - see publication for complete details, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2008 |
Radiation | Monochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 16233 / Num. obs: 16233 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Starting model: P21 crystal structure obtained as described in publication Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.31 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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