+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13892 | |||||||||
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Title | Spraguea lophii ribosome | |||||||||
Map data | Best overall map for both LSU and SSU | |||||||||
Sample |
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Keywords | Microsporidia / RIBOSOME | |||||||||
Function / homology | Function and homology information translation regulator activity / cytosolic ribosome / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome ...translation regulator activity / cytosolic ribosome / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Spraguea lophii 42_110 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
Authors | Gil Diez P / McLaren M | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state Authors: McLaren M / Conners R / Isupov MN / Gil-Diez P / Gambelli L / Gold VAM / Walter A / Connell SR / Williams B / Daum B | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13892.map.gz | 108.8 MB | EMDB map data format | |
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Header (meta data) | emd-13892-v30.xml emd-13892.xml | 116.9 KB 116.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13892_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_13892.png | 74.5 KB | ||
Filedesc metadata | emd-13892.cif.gz | 18.7 KB | ||
Others | emd_13892_additional_1.map.gz emd_13892_additional_2.map.gz emd_13892_additional_3.map.gz emd_13892_additional_4.map.gz emd_13892_additional_5.map.gz | 97.9 MB 64.1 MB 65 MB 60.1 MB 105.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13892 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13892 | HTTPS FTP |
-Related structure data
Related structure data | 7qcaMC 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_13892.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Best overall map for both LSU and SSU | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.054 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Overall map before postprocessing
File | emd_13892_additional_1.map | ||||||||||||
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Annotation | Overall map before postprocessing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The map after deepenhancer with masked LSU
File | emd_13892_additional_2.map | ||||||||||||
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Annotation | The map after deepenhancer with masked LSU | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The map after deepenhancer with masked SSU body
File | emd_13892_additional_3.map | ||||||||||||
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Annotation | The map after deepenhancer with masked SSU body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The map after deepenhancer with masked SSU head
File | emd_13892_additional_4.map | ||||||||||||
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Annotation | The map after deepenhancer with masked SSU head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The map processed with the mask centered at L1 stalk region
File | emd_13892_additional_5.map | ||||||||||||
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Annotation | The map processed with the mask centered at L1 stalk region | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosome
+Supramolecule #1: Ribosome
+Macromolecule #1: RNA 23S
+Macromolecule #2: RNA 5S
+Macromolecule #41: RNA SSU
+Macromolecule #3: 60S ribosomal protein L8
+Macromolecule #4: uL15 LAA
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L3
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L31
+Macromolecule #10: 60S ribosomal protein L6
+Macromolecule #11: 60S ribosomal protein L32
+Macromolecule #12: 60S ribosomal protein L7
+Macromolecule #13: 60S ribosomal protein L35a
+Macromolecule #14: 60S ribosomal protein L8
+Macromolecule #15: Ribosomal protein L34
+Macromolecule #16: 60S ribosomal protein L9
+Macromolecule #17: Ribosomal L29 protein
+Macromolecule #18: S60 ribosomal protein L10
+Macromolecule #19: 60S ribosomal protein L36
+Macromolecule #20: 60S ribosomal protein L11
+Macromolecule #21: eL37 LJJ
+Macromolecule #22: 60S ribosomal protein L13
+Macromolecule #23: 60S ribosomal protein L39
+Macromolecule #24: eL14 LM0
+Macromolecule #25: Ubiquitin
+Macromolecule #26: Ribosomal protein L15
+Macromolecule #27: Ribosomal protein L13A
+Macromolecule #28: 60S ribosomal protein L44
+Macromolecule #29: 60S ribosomal protein L17
+Macromolecule #30: 60S ribosomal protein L37a
+Macromolecule #31: 60S ribosomal protein L18
+Macromolecule #32: 60S ribosomal protein L19
+Macromolecule #33: 60S ribosomal protein L20
+Macromolecule #34: 60s ribosomal protein L21
+Macromolecule #35: 60S ribosomal protein L22
+Macromolecule #36: Ribosomal protein L23
+Macromolecule #37: Ribosomal protein L24E
+Macromolecule #38: 60S ribosomal protein L23a
+Macromolecule #39: 60S ribosomal protein L26
+Macromolecule #40: 60S ribosomal protein L27
+Macromolecule #42: 40S ribosomal protein S0
+Macromolecule #43: 40S ribosomal protein S26
+Macromolecule #44: eS1 SB0
+Macromolecule #45: eS27 SBB
+Macromolecule #46: 40S ribosomal protein S2
+Macromolecule #47: eS28 SCC
+Macromolecule #48: 40S ribosomal protein S3
+Macromolecule #49: 40S ribosomal protein S29
+Macromolecule #50: 40S ribosomal protein S4
+Macromolecule #51: eS30 SEE
+Macromolecule #52: 40S ribosomal protein S5
+Macromolecule #53: Ubiquitin/40s ribosomal protein S27a fusion
+Macromolecule #54: 40S ribosomal protein S6
+Macromolecule #55: Guanine nucleotide binding protein beta subunit
+Macromolecule #56: 40S ribosomal protein S7
+Macromolecule #57: 40S ribosomal protein S8
+Macromolecule #58: 40S ribosomal protein S9
+Macromolecule #59: 40S ribosomal protein S10
+Macromolecule #60: 40S ribosomal protein S11
+Macromolecule #61: 40S ribosomal protein S12
+Macromolecule #62: 40S ribosomal protein S13
+Macromolecule #63: 40S ribosomal protein S14
+Macromolecule #64: Ribosomal protein S19
+Macromolecule #65: 40S ribosomal protein S16
+Macromolecule #66: eS17 SR0
+Macromolecule #67: 40S ribosomal protein S18
+Macromolecule #68: 40S Ribosomal protein S19
+Macromolecule #69: 40S ribosomal protein S20
+Macromolecule #70: Ribosomal protein S21E
+Macromolecule #71: 40S ribosomal protein S15A
+Macromolecule #72: uS12 SX0
+Macromolecule #73: 40s ribosomal protein s24
+Macromolecule #74: 40S ribosomal protein S25
+Macromolecule #75: POTASSIUM ION
+Macromolecule #76: MAGNESIUM ION
+Macromolecule #77: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solution with HEPES, Potassium Acetate and Magnesium acetate was autoclaved. DTT was added fresh just before sample preparation. | |||||||||||||||
Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: 20 mA. Carbon coated grid | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force -1 and blot time 4 s. | |||||||||||||||
Details | Monomeric ribosomes from Spraguea lophii |
-Electron microscopy #1
Microscope | TFS 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: 2.5 µm / Nominal defocus min: 1.2 µm |
Microscopy ID | 1 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscope | TFS TALOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Microscopy ID | 1 |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 41.34 e/Å2 |