+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30433 | ||||||||||||
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Title | Cryo-EM structure of 80S ribosome from mouse testis | ||||||||||||
Map data | 80S ribosome from mouse testis | ||||||||||||
Sample |
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Keywords | RPL39L / testis ribosome / Cryo-EM / RIBOSOME | ||||||||||||
Function / homology | Function and homology information TNFR1-mediated ceramide production / 5.8S rRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / positive regulation of amide metabolic process / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) ...TNFR1-mediated ceramide production / 5.8S rRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / positive regulation of amide metabolic process / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / Formation of a pool of free 40S subunits / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SRP-dependent cotranslational protein targeting to membrane / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Dual incision in TC-NER / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||||||||
Authors | Huo YG / He X | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nature / Year: 2022 Title: A male germ-cell-specific ribosome controls male fertility. Authors: Huiling Li / Yangao Huo / Xi He / Liping Yao / Hao Zhang / Yiqiang Cui / Huijuan Xiao / Wenxiu Xie / Dejiu Zhang / Yue Wang / Shu Zhang / Haixia Tu / Yiwei Cheng / Yueshuai Guo / Xintao Cao ...Authors: Huiling Li / Yangao Huo / Xi He / Liping Yao / Hao Zhang / Yiqiang Cui / Huijuan Xiao / Wenxiu Xie / Dejiu Zhang / Yue Wang / Shu Zhang / Haixia Tu / Yiwei Cheng / Yueshuai Guo / Xintao Cao / Yunfei Zhu / Tao Jiang / Xuejiang Guo / Yan Qin / Jiahao Sha / Abstract: Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis. Male germ cell development involves complex ...Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis. Male germ cell development involves complex translational regulation during sperm formation. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, Ribosome, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (Ribosome) protein RPL39. Deletion of Ribosome in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that Ribosome features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with Ribosome. Ribosome predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of Ribosome were not replaceable by Ribosome. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30433.map.gz | 41.9 MB | EMDB map data format | |
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Header (meta data) | emd-30433-v30.xml emd-30433.xml | 95.6 KB 95.6 KB | Display Display | EMDB header |
Images | emd_30433.png | 72.1 KB | ||
Filedesc metadata | emd-30433.cif.gz | 19.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30433 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30433 | HTTPS FTP |
-Validation report
Summary document | emd_30433_validation.pdf.gz | 507.8 KB | Display | EMDB validaton report |
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Full document | emd_30433_full_validation.pdf.gz | 507.4 KB | Display | |
Data in XML | emd_30433_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_30433_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30433 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30433 | HTTPS FTP |
-Related structure data
Related structure data | 7cpvMC 7cpuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30433.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 80S ribosome from mouse testis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Mus musculus 80S ribosome from testis
+Supramolecule #1: Mus musculus 80S ribosome from testis
+Macromolecule #1: 60S ribosomal protein L8
+Macromolecule #2: 60S ribosomal protein L3
+Macromolecule #3: 60S ribosomal protein L4
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: 60S ribosomal protein L7
+Macromolecule #7: 60S ribosomal protein L7a
+Macromolecule #8: 60S ribosomal protein L9
+Macromolecule #9: 60S ribosomal protein L10-like
+Macromolecule #10: 60S ribosomal protein L11
+Macromolecule #11: 60S ribosomal protein L13
+Macromolecule #12: 60S ribosomal protein L14
+Macromolecule #13: 60S ribosomal protein L15
+Macromolecule #14: 60S ribosomal protein L13a
+Macromolecule #15: 60S ribosomal protein L17
+Macromolecule #16: 60S ribosomal protein L18
+Macromolecule #17: 60S ribosomal protein L19
+Macromolecule #18: 60S ribosomal protein L18a
+Macromolecule #19: 60S ribosomal protein L21
+Macromolecule #20: 60S ribosomal protein L22
+Macromolecule #21: 60S ribosomal protein L23
+Macromolecule #22: 60S ribosomal protein L24
+Macromolecule #23: 60S ribosomal protein L23a
+Macromolecule #24: 60S ribosomal protein L26
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: 60S ribosomal protein L27a
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: 60S ribosomal protein L30
+Macromolecule #29: 60S ribosomal protein L31
+Macromolecule #30: 60S ribosomal protein L32
+Macromolecule #31: 60S ribosomal protein L35a
+Macromolecule #32: 60S ribosomal protein L34
+Macromolecule #33: 60S ribosomal protein L35
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: 60S ribosomal protein L37
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: Ribosomal protein L39-like
+Macromolecule #38: Ubiquitin-60S ribosomal protein L40
+Macromolecule #39: 60S ribosomal protein L41
+Macromolecule #40: 60S ribosomal protein L36a
+Macromolecule #41: 60S ribosomal protein L37a
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #47: 40S ribosomal protein SA
+Macromolecule #48: 40S ribosomal protein S3a
+Macromolecule #49: 40S ribosomal protein S3
+Macromolecule #50: 40S ribosomal protein S4, X isoform
+Macromolecule #51: 40S ribosomal protein S5
+Macromolecule #52: 40S ribosomal protein S7
+Macromolecule #53: 40S ribosomal protein S8
+Macromolecule #54: 40S ribosomal protein S10
+Macromolecule #55: 40S ribosomal protein S11
+Macromolecule #56: 40S ribosomal protein S15
+Macromolecule #57: 40S ribosomal protein S16
+Macromolecule #58: 40S ribosomal protein S17
+Macromolecule #59: 40S ribosomal protein S18
+Macromolecule #60: 40S ribosomal protein S19
+Macromolecule #61: 40S ribosomal protein S20
+Macromolecule #62: 40S ribosomal protein S21
+Macromolecule #63: 40S ribosomal protein S23
+Macromolecule #64: 40S ribosomal protein S26
+Macromolecule #65: 40S ribosomal protein S28
+Macromolecule #66: 40S ribosomal protein S29
+Macromolecule #67: Receptor of activated protein C kinase 1
+Macromolecule #68: 40S ribosomal protein S2
+Macromolecule #69: 40S ribosomal protein S6
+Macromolecule #70: 40S ribosomal protein S9
+Macromolecule #71: 40S ribosomal protein S13
+Macromolecule #72: 40S ribosomal protein S14
+Macromolecule #73: 40S ribosomal protein S15a
+Macromolecule #74: 40S ribosomal protein S24
+Macromolecule #75: 40S ribosomal protein S25
+Macromolecule #76: 40S ribosomal protein S27
+Macromolecule #77: 40S ribosomal protein S30
+Macromolecule #43: Mus musculus 28S ribosomal RNA
+Macromolecule #44: Mus musculus 5S ribosomal RNA
+Macromolecule #45: Mus musculus 5.8S ribosomal RNA
+Macromolecule #46: Mus musculus 18S ribosomal RNA
+Macromolecule #78: Met-tRNA
+Macromolecule #79: MAGNESIUM ION
+Macromolecule #80: ZINC ION
+Macromolecule #81: water
-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 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: 6ek0 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100403 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |