+Open data
-Basic information
Entry | Database: PDB / ID: 4xmm | ||||||||||||
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Title | Structure of the yeast coat nucleoporin complex, space group C2 | ||||||||||||
Components |
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Keywords | Transport Protein/Immune System / Structural protein / Immune System / Transport Protein-Immune System complex | ||||||||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / regulation of TORC1 signaling / nuclear pore outer ring / telomere tethering at nuclear periphery / 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 / tRNA export from nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / 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 / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / protein export from nucleus / cellular response to amino acid starvation / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / protein transport / chromosome, telomeric region / nuclear membrane / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.384 Å | ||||||||||||
Authors | Stuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2015 Title: Nuclear pores. Architecture of the nuclear pore complex coat. Authors: Stuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xmm.cif.gz | 623.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xmm.ent.gz | 485.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xmm_validation.pdf.gz | 479 KB | Display | wwPDB validaton report |
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Full document | 4xmm_full_validation.pdf.gz | 527.5 KB | Display | |
Data in XML | 4xmm_validation.xml.gz | 66 KB | Display | |
Data in CIF | 4xmm_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/4xmm ftp://data.pdbj.org/pub/pdb/validation_reports/xm/4xmm | HTTPS FTP |
-Related structure data
Related structure data | 4xmnC 3f3fS 3f7fS 3ikoS 3pgfS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 33082.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04491 |
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#2: Protein | Mass: 74618.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP145, RAT10, YGL092W / Production host: Escherichia coli (E. coli) References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Protein | Mass: 39170.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SEH1, YGL100W / Production host: Escherichia coli (E. coli) / References: UniProt: P53011 |
#4: Protein | Mass: 81568.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP85, RAT9, YJR042W, J1624 / Production host: Escherichia coli (E. coli) / References: UniProt: P46673 |
#5: Protein | Mass: 121577.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729 |
#6: Protein | Mass: 52059.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / References: UniProt: P52891 |
-Antibody , 2 types, 2 molecules HL
#7: Antibody | Mass: 28977.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#8: Antibody | Mass: 23588.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.92 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 20000, ethanol, MES / PH range: 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 7.384→70 Å / Num. obs: 10375 / % possible obs: 99 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 7.384→7.8 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.4 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IKO, 3F3F, 3F7F, and 3PGF Resolution: 7.384→67.516 Å / SU ML: 1.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.3 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 7.384→67.516 Å
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Refine LS restraints |
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LS refinement shell |
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