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Yorodumi- EMDB-19198: Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19198 | ||||||||||||
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Title | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Ribosome / Membrane protein / Translocon / Transport | ||||||||||||
Function / homology | Function and homology information L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / muscle organ morphogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking ...L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / muscle organ morphogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / positive regulation of growth hormone secretion / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / positive regulation of organ growth / melanosome membrane / clathrin-dependent endocytosis / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / insulin secretion / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / G1 to G0 transition / : / cytoplasmic microtubule / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / synaptic vesicle endocytosis / protein-RNA complex assembly / protein transmembrane transporter activity / cellular response to actinomycin D / rough endoplasmic reticulum / endoplasmic reticulum unfolded protein response / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / ribosomal large subunit biogenesis / skeletal system development / positive regulation of translation / mitochondrial membrane / phospholipid binding / positive regulation of insulin secretion / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / glucose metabolic process / large ribosomal subunit / unfolded protein binding / protein folding / presynapse / ribosome binding / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / carbohydrate binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Canis lupus familiaris (dog) / Oryctolagus cuniculus (rabbit) / Bos taurus (cattle) / Oryctolagus (mammal) / Sus scrofa (pig) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.78574 Å | ||||||||||||
Authors | Lewis AJO / Hegde RS | ||||||||||||
Funding support | United Kingdom, United States, 3 items
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Citation | Journal: Biochem J / Year: 2021 Title: New tools for automated cryo-EM single-particle analysis in RELION-4.0. Authors: Dari Kimanius / Liyi Dong / Grigory Sharov / Takanori Nakane / Sjors H W Scheres / Abstract: We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient ...We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient descent algorithm with adaptive moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on 12 publicly available cryo-EM data sets. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19198.map.gz | 263.5 MB | EMDB map data format | |
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Header (meta data) | emd-19198-v30.xml emd-19198.xml | 78.7 KB 78.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19198_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_19198.png | 156.7 KB | ||
Filedesc metadata | emd-19198.cif.gz | 16.8 KB | ||
Others | emd_19198_half_map_1.map.gz emd_19198_half_map_2.map.gz | 225.2 MB 225.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19198 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19198 | HTTPS FTP |
-Related structure data
Related structure data | 8rjdMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19198.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.33981 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_19198_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19198_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 80S ribosome translating a stalled, two-TMD nascent chain (derive...
+Supramolecule #1: 80S ribosome translating a stalled, two-TMD nascent chain (derive...
+Macromolecule #1: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #2: Protein transport protein Sec61 subunit beta
+Macromolecule #3: Protein transport protein Sec61 subunit gamma
+Macromolecule #4: Stress-associated endoplasmic reticulum protein
+Macromolecule #5: Translocon-associated protein subunit alpha
+Macromolecule #6: Translocon-associated protein subunit beta
+Macromolecule #7: Translocon-associated protein subunit gamma
+Macromolecule #8: Translocon-associated protein subunit delta
+Macromolecule #9: Calnexin
+Macromolecule #10: Ribosomal protein L8
+Macromolecule #11: Nascent chain
+Macromolecule #12: Large ribosomal subunit protein uL4
+Macromolecule #13: Ribosomal_L18_c domain-containing protein
+Macromolecule #14: 60S ribosomal protein L6
+Macromolecule #15: Ribosomal Protein uL30
+Macromolecule #16: 60S ribosomal protein L7a
+Macromolecule #17: 60S ribosomal protein L9
+Macromolecule #18: 60S ribosomal protein L10
+Macromolecule #19: 60S ribosomal protein L11
+Macromolecule #21: 60S ribosomal protein L13
+Macromolecule #22: 60S ribosomal protein L14
+Macromolecule #23: Ribosomal protein L15
+Macromolecule #24: 60S ribosomal protein L13a
+Macromolecule #25: uL22
+Macromolecule #26: Ribosomal protein L18
+Macromolecule #27: Ribosomal protein L19
+Macromolecule #28: 60S ribosomal protein L18a
+Macromolecule #29: 60S ribosomal protein L21
+Macromolecule #30: Large ribosomal subunit protein eL22
+Macromolecule #31: Ribosomal protein L23
+Macromolecule #32: Ribosomal protein L24
+Macromolecule #33: Large ribosomal subunit protein uL23 N-terminal domain-containing...
+Macromolecule #34: Ribosomal protein L26
+Macromolecule #35: 60S ribosomal protein L27
+Macromolecule #36: 60S ribosomal protein L27a
+Macromolecule #37: 60S ribosomal protein L29
+Macromolecule #38: Large ribosomal subunit protein eL30
+Macromolecule #39: 60S ribosomal protein L31
+Macromolecule #40: Ribosomal protein L32
+Macromolecule #41: 60S ribosomal protein L35a
+Macromolecule #42: 60S ribosomal protein L34
+Macromolecule #43: 60S ribosomal protein L35
+Macromolecule #44: 60S ribosomal protein L36
+Macromolecule #45: Ribosomal protein L37
+Macromolecule #46: Large ribosomal subunit protein eL38
+Macromolecule #47: 60S ribosomal protein L39-like
+Macromolecule #48: eL40
+Macromolecule #49: 60S ribosomal protein L41
+Macromolecule #50: 60S ribosomal protein L36a-like
+Macromolecule #51: 60S ribosomal protein L37a
+Macromolecule #53: 60S ribosomal protein L28
+Macromolecule #56: Ribosomal protein L3
+Macromolecule #20: 28S rRNA
+Macromolecule #52: P-site tRNA
+Macromolecule #54: 5S rRNA
+Macromolecule #55: 5.8S rRNA
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.9000000000000001 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 17540 / Average electron dose: 54.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8rjd: |