+Open data
-Basic information
Entry | Database: PDB / ID: 7cpu | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of 80S ribosome from mouse kidney | ||||||||||||
Components |
| ||||||||||||
Keywords | RIBOSOME / 80S mouse ribosome / protein translation / RPL39 / RPL39L / kidney ribosome | ||||||||||||
Function / homology | Function and homology information TNFR1-mediated ceramide production / 5.8S rRNA binding / Protein hydroxylation / translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of amide metabolic process / 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 / Protein hydroxylation / translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of amide metabolic process / 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 pyruvate metabolism / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / 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) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / 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 / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 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 / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Translesion synthesis by POLK / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Spry regulation of FGF signaling / SRP-dependent cotranslational protein targeting to membrane / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / 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 / Termination of translesion DNA synthesis / Protein methylation / Inactivation of CSF3 (G-CSF) signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / PINK1-PRKN Mediated Mitophagy / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / 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 / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of necroptotic cell death / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å | ||||||||||||
Authors | Huo, Y.G. / He, X. / Jiang, T. / Qin, Y. / Guo, X.J. / Sha, J.H. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7cpu.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7cpu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7cpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cpu_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7cpu_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7cpu_validation.xml.gz | 308.3 KB | Display | |
Data in CIF | 7cpu_validation.cif.gz | 546.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/7cpu ftp://data.pdbj.org/pub/pdb/validation_reports/cp/7cpu | HTTPS FTP |
-Related structure data
Related structure data | 30432MC 7cpvC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+60S ribosomal protein ... , 40 types, 40 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...
+40S ribosomal protein ... , 30 types, 30 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSNSOSWSYSZSbSe
-Protein , 3 types, 3 molecules LmSgLl
#39: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984 |
---|---|
#66: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68040 |
#78: Protein | Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q505A8 |
-Mus musculus ... , 4 types, 4 molecules L5L7L8S2
#44: RNA chain | Mass: 1530907.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
---|---|
#45: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 396138 |
#46: RNA chain | Mass: 50795.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1059793825 |
#47: RNA chain | Mass: 603101.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-RNA chain , 1 types, 1 molecules S6
#77: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
---|
-Non-polymers , 3 types, 297 molecules
#79: Chemical | ChemComp-MG / #80: Chemical | ChemComp-ZN / #81: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mus musculus 80S ribosome from kidney / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280287 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6EK0 6ek0 Accession code: 6EK0 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.58 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|