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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30432 | ||||||||||||
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Title | Cryo-EM structure of 80S ribosome from mouse kidney | ||||||||||||
![]() | ribosome from mouse kidney | ||||||||||||
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![]() | 80S mouse ribosome / protein translation / RPL39 / RPL39L / kidney ribosome / RIBOSOME | ||||||||||||
Function / homology | ![]() 5.8S rRNA binding / TNFR1-mediated ceramide production / Protein hydroxylation / positive regulation of amide metabolic process / Formation of the ternary complex, and subsequently, the 43S complex / 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 ...5.8S rRNA binding / TNFR1-mediated ceramide production / Protein hydroxylation / positive regulation of amide metabolic process / Formation of the ternary complex, and subsequently, the 43S complex / 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 / 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 / Regulation of expression of SLITs and ROBOs / 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 / 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 / Formation of a pool of free 40S subunits / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / 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 / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / SRP-dependent cotranslational protein targeting to membrane / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Dual incision in TC-NER / Oncogene Induced Senescence / PINK1-PRKN Mediated Mitophagy / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Inactivation of CSF3 (G-CSF) signaling / 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) / EGFR downregulation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Protein methylation Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | ||||||||||||
![]() | Huo YG / He X | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 96.4 KB 96.4 KB | Display Display | ![]() |
Images | ![]() | 66 KB | ||
Filedesc metadata | ![]() | 19.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cpuMC ![]() 7cpvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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 | ribosome from mouse kidney | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
+Entire : Mus musculus 80S ribosome from kidney
+Supramolecule #1: Mus musculus 80S ribosome from kidney
+Macromolecule #1: 60S ribosomal protein L8
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 40S ribosomal protein S3a
+Macromolecule #5: 60S ribosomal protein L4
+Macromolecule #6: 60S ribosomal protein L5
+Macromolecule #7: 60S ribosomal protein L6
+Macromolecule #8: 60S ribosomal protein L7
+Macromolecule #9: 60S ribosomal protein L7a
+Macromolecule #10: 60S ribosomal protein L9
+Macromolecule #11: 60S ribosomal protein L10
+Macromolecule #12: 60S ribosomal protein L11
+Macromolecule #13: 60S ribosomal protein L13
+Macromolecule #14: 60S ribosomal protein L14
+Macromolecule #15: 60S ribosomal protein L15
+Macromolecule #16: 60S ribosomal protein L13a
+Macromolecule #17: 60S ribosomal protein L17
+Macromolecule #18: 60S ribosomal protein L18
+Macromolecule #19: 60S ribosomal protein L19
+Macromolecule #20: 60S ribosomal protein L18a
+Macromolecule #21: 60S ribosomal protein L21
+Macromolecule #22: 60S ribosomal protein L22
+Macromolecule #23: 60S ribosomal protein L23
+Macromolecule #24: 60S ribosomal protein L24
+Macromolecule #25: 60S ribosomal protein L23a
+Macromolecule #26: 60S ribosomal protein L26
+Macromolecule #27: 60S ribosomal protein L27
+Macromolecule #28: 60S ribosomal protein L27a
+Macromolecule #29: 60S ribosomal protein L29
+Macromolecule #30: 60S ribosomal protein L30
+Macromolecule #31: 60S ribosomal protein L31
+Macromolecule #32: 60S ribosomal protein L32
+Macromolecule #33: 60S ribosomal protein L35a
+Macromolecule #34: 60S ribosomal protein L34
+Macromolecule #35: 60S ribosomal protein L35
+Macromolecule #36: 60S ribosomal protein L36
+Macromolecule #37: 60S ribosomal protein L37
+Macromolecule #38: 60S ribosomal protein L38
+Macromolecule #39: Ubiquitin-60S ribosomal protein L40
+Macromolecule #40: 60S ribosomal protein L41
+Macromolecule #41: 60S ribosomal protein L36a
+Macromolecule #42: 60S ribosomal protein L37a
+Macromolecule #43: 60S ribosomal protein L28
+Macromolecule #48: 40S ribosomal protein S3
+Macromolecule #49: 40S ribosomal protein S4, X isoform
+Macromolecule #50: 40S ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S7
+Macromolecule #52: 40S ribosomal protein S8
+Macromolecule #53: 40S ribosomal protein S10
+Macromolecule #54: 40S ribosomal protein S11
+Macromolecule #55: 40S ribosomal protein S15
+Macromolecule #56: 40S ribosomal protein S16
+Macromolecule #57: 40S ribosomal protein S17
+Macromolecule #58: 40S ribosomal protein S18
+Macromolecule #59: 40S ribosomal protein S19
+Macromolecule #60: 40S ribosomal protein S20
+Macromolecule #61: 40S ribosomal protein S21
+Macromolecule #62: 40S ribosomal protein S23
+Macromolecule #63: 40S ribosomal protein S26
+Macromolecule #64: 40S ribosomal protein S28
+Macromolecule #65: 40S ribosomal protein S29
+Macromolecule #66: Receptor of activated protein C kinase 1
+Macromolecule #67: 40S ribosomal protein S2
+Macromolecule #68: 40S ribosomal protein S6
+Macromolecule #69: 40S ribosomal protein S9
+Macromolecule #70: 40S ribosomal protein S13
+Macromolecule #71: 40S ribosomal protein S14
+Macromolecule #72: 40S ribosomal protein S15a
+Macromolecule #73: 40S ribosomal protein S24
+Macromolecule #74: 40S ribosomal protein S25
+Macromolecule #75: 40S ribosomal protein S27
+Macromolecule #76: 40S ribosomal protein S30
+Macromolecule #78: Ribosomal protein L39
+Macromolecule #44: Mus musculus 28S ribosomal RNA
+Macromolecule #45: Mus musculus 5S ribosomal RNA
+Macromolecule #46: Mus musculus 5.8S ribosomal RNA
+Macromolecule #47: Mus musculus 18S ribosomal RNA
+Macromolecule #77: tRNA
+Macromolecule #79: MAGNESIUM ION
+Macromolecule #80: ZINC ION
+Macromolecule #81: water
-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 Component:
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280287 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |