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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Yeast SDD1 Disome with Mbf1 | |||||||||
![]() | Yeast SDD1 Disome with Mbf1 - composite map | |||||||||
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![]() | ribosome / quality control / frame shifting / collision | |||||||||
Function / homology | ![]() maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of amino acid metabolic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / Ub-specific processing proteases / ribosomal subunit export from nucleus / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transcription coactivator activity / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Denk T / Beckmann R | |||||||||
Funding support | ![]()
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![]() | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() ![]() ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 125.6 KB 125.6 KB | Display Display | ![]() |
Images | ![]() | 86.1 KB | ||
Filedesc metadata | ![]() | 21.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f9sMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Yeast SDD1 Disome with Mbf1 - composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : glutaraldehyde crosslinked trisome fraction after sucrose density...
+Supramolecule #1: glutaraldehyde crosslinked trisome fraction after sucrose density...
+Supramolecule #2: SDD1
+Supramolecule #3: mRNA
+Supramolecule #4: Yeast Disome
+Macromolecule #1: Uncharacterized protein YEL057C
+Macromolecule #3: Multiprotein-bridging factor 1
+Macromolecule #8: 60S ribosomal protein L6-B
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11-A
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-A
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L21-A
+Macromolecule #23: 60S ribosomal protein L23-A
+Macromolecule #24: 60S ribosomal protein L43-A
+Macromolecule #25: 60S ribosomal protein L42-A
+Macromolecule #26: 60S ribosomal protein L41-A
+Macromolecule #27: Ubiquitin-60S ribosomal protein L40
+Macromolecule #28: 60S ribosomal protein L39
+Macromolecule #29: 60S ribosomal protein L38
+Macromolecule #30: 60S ribosomal protein L37-A
+Macromolecule #31: 60S ribosomal protein L36-A
+Macromolecule #32: 60S ribosomal protein L35-A
+Macromolecule #33: 60S ribosomal protein L34-A
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L31-A
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: 60S ribosomal protein L29
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: 60S ribosomal protein L27-A
+Macromolecule #41: 60S ribosomal protein L26-A
+Macromolecule #42: 60S ribosomal protein L25
+Macromolecule #43: 60S ribosomal protein L24-A
+Macromolecule #44: 60S ribosomal protein L22-A
+Macromolecule #45: 60S ribosomal protein L2-A
+Macromolecule #46: 60S ribosomal protein L3
+Macromolecule #47: 60S ribosomal protein L4-A
+Macromolecule #48: 60S ribosomal protein L5
+Macromolecule #50: Small ribosomal subunit protein eS26A
+Macromolecule #51: 40S ribosomal protein S27-A
+Macromolecule #52: Small ribosomal subunit protein eS28B
+Macromolecule #53: Small ribosomal subunit protein uS14A
+Macromolecule #54: 40S ribosomal protein S30-A
+Macromolecule #55: Ubiquitin
+Macromolecule #56: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #57: 40S ribosomal protein S0-A
+Macromolecule #58: 40S ribosomal protein S1-A
+Macromolecule #59: 40S ribosomal protein S2
+Macromolecule #60: Small ribosomal subunit protein uS3
+Macromolecule #61: 40S ribosomal protein S4-A
+Macromolecule #62: 40S ribosomal protein S5
+Macromolecule #63: 40S ribosomal protein S6-A
+Macromolecule #64: 40S ribosomal protein S7-A
+Macromolecule #65: 40S ribosomal protein S8-A
+Macromolecule #66: 40S ribosomal protein S9-A
+Macromolecule #67: 40S ribosomal protein S10-A
+Macromolecule #68: 40S ribosomal protein S11-A
+Macromolecule #69: 40S ribosomal protein S12
+Macromolecule #70: 40S ribosomal protein S13
+Macromolecule #71: 40S ribosomal protein S14-A
+Macromolecule #72: 40S ribosomal protein S15
+Macromolecule #73: 40S ribosomal protein S16-A
+Macromolecule #74: 40S ribosomal protein S17-B
+Macromolecule #75: 40S ribosomal protein S18-A
+Macromolecule #76: 40S ribosomal protein S19-A
+Macromolecule #77: Small ribosomal subunit protein uS10
+Macromolecule #78: Small ribosomal subunit protein eS21A
+Macromolecule #79: 40S ribosomal protein S22-A
+Macromolecule #80: 40S ribosomal protein S23-A
+Macromolecule #81: 40S ribosomal protein S24-A
+Macromolecule #82: 40S ribosomal protein S25-A
+Macromolecule #83: 40S ribosomal protein S28-A
+Macromolecule #84: 40S ribosomal protein S14-B
+Macromolecule #85: 40S ribosomal protein S17-A
+Macromolecule #86: 60S ribosomal protein L6-A
+Macromolecule #89: 60S acidic ribosomal protein P0
+Macromolecule #90: 60S ribosomal protein L12-A
+Macromolecule #2: mRNA
+Macromolecule #4: tRNA P-site, stalled
+Macromolecule #5: Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1)
+Macromolecule #6: Saccharomyces cerevisiae S288C 5.8S ribosomal RNA
+Macromolecule #7: Saccharomyces cerevisiae S288C 5S ribosomal RNA
+Macromolecule #49: Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1)
+Macromolecule #87: Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1) with m...
+Macromolecule #88: tRNA
+Macromolecule #91: tRNA
+Macromolecule #92: MAGNESIUM ION
+Macromolecule #93: ZINC ION
+Macromolecule #94: POTASSIUM ION
+Macromolecule #95: SPERMIDINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Number classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: OTHER Details: This is a composite map. The masked resolution is given as calculated by Phenix. Number images used: 189911 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |