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- PDB-4xmn: Structure of the yeast coat nucleoporin complex, space group P212121 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xmn | ||||||
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Title | Structure of the yeast coat nucleoporin complex, space group P212121 | ||||||
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![]() | PROTEIN TRANSPORT / STRUCTURAL 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 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 / 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 / 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 / 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 / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stuwe, T. / Correia, A.R. / Lin, D.H. / Paduch, M. / Lu, V.T. / Kossiakoff, A.A. / Hoelz, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 492.1 KB | Display | ![]() |
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PDB format | ![]() | 373.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xmmC ![]() 3f7fS ![]() 3ikoS ![]() 3pgfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 5 types, 5 molecules ABFED
#1: Protein | Mass: 33129.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: ![]() ![]() |
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#2: Protein | Mass: 75087.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NUP145, RAT10, YGL092W / Production host: ![]() ![]() References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Protein | Mass: 52434.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NUP84, YDL116W / Production host: ![]() ![]() |
#4: Protein | Mass: 121607.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: ![]() ![]() |
#5: Protein | Mass: 79188.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NUP85, RAT9, YJR042W, J1624 / Production host: ![]() ![]() |
-Antibody , 2 types, 2 molecules LH
#6: Antibody | Mass: 23461.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Description: phage display library / Production host: ![]() ![]() |
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#7: Antibody | Mass: 28615.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Description: obtained from phage display library / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.62 Å3/Da / Density % sol: 78.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 20000, ethanol, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 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: 7.6→50 Å / Num. obs: 22082 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 13.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IKO, 3F7F, 3PGF Resolution: 7.6→49.606 Å / SU ML: 1.02 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 7.6→49.606 Å
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Refine LS restraints |
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LS refinement shell |
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