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- PDB-7cpv: Cryo-EM structure of 80S ribosome from mouse testis -

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Basic information

Entry
Database: PDB / ID: 7cpv
TitleCryo-EM structure of 80S ribosome from mouse testis
Components
  • (40S ribosomal protein ...) x 30
  • (60S ribosomal protein ...) x 40
  • (Mus musculus ...) x 4
  • Met-tRNA
  • Receptor of activated protein C kinase 1
  • Ribosomal protein L39-like
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / RPL39L / testis ribosome / Cryo-EM
Function / homology
Function and homology information


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
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / : / Ribosomal protein S17e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL16-like / Small ribosomal subunit protein eS1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL39-like / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsHuo, Y.G. / He, X. / Jiang, T. / Qin, Y. / Guo, X.J. / Sha, J.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31890784 China
National Natural Science Foundation of China (NSFC)81701511 China
National Natural Science Foundation of China (NSFC)31830043 China
CitationJournal: 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
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein L7
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: 60S ribosomal protein L10-like
LJ: 60S ribosomal protein L11
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: 60S ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: Ribosomal protein L39-like
Lm: Ubiquitin-60S ribosomal protein L40
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
L5: Mus musculus 28S ribosomal RNA
L7: Mus musculus 5S ribosomal RNA
L8: Mus musculus 5.8S ribosomal RNA
S2: Mus musculus 18S ribosomal RNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SD: 40S ribosomal protein S3
SE: 40S ribosomal protein S4, X isoform
SF: 40S ribosomal protein S5
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SX: 40S ribosomal protein S23
Sa: 40S ribosomal protein S26
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Sg: Receptor of activated protein C kinase 1
SC: 40S ribosomal protein S2
SG: 40S ribosomal protein S6
SJ: 40S ribosomal protein S9
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SW: 40S ribosomal protein S15a
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sb: 40S ribosomal protein S27
Se: 40S ribosomal protein S30
S6: Met-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,679,385332
Polymers3,672,92378
Non-polymers6,461254
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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60S ribosomal protein ... , 40 types, 40 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#1: Protein 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#2: Protein 60S ribosomal protein L3 / J1 protein


Mass: 46212.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#3: Protein 60S ribosomal protein L4


Mass: 47259.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#4: Protein 60S ribosomal protein L5


Mass: 34464.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#5: Protein 60S ribosomal protein L6 / TAX-responsive enhancer element-binding protein 107 / TAXREB107


Mass: 33593.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47911
#6: Protein 60S ribosomal protein L7


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#7: Protein 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 30042.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#8: Protein 60S ribosomal protein L9


Mass: 21917.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#9: Protein 60S ribosomal protein L10-like


Mass: 24612.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P86048
#10: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#11: Protein 60S ribosomal protein L13 / A52


Mass: 24364.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#12: Protein 60S ribosomal protein L14


Mass: 23620.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#13: Protein 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#14: Protein 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 23519.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#15: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWZ7
#16: Protein 60S ribosomal protein L18


Mass: 21698.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#17: Protein 60S ribosomal protein L19 / 60S ribosomal protein L19 isoform 1


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#18: Protein 60S ribosomal protein L18a


Mass: 20778.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#19: Protein 60S ribosomal protein L21


Mass: 18624.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQM8
#20: Protein 60S ribosomal protein L22 / 60S ribosomal protein L22 isoform a / Heparin-binding protein HBp15


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#21: Protein 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#22: Protein 60S ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#23: Protein 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#24: Protein 60S ribosomal protein L26 / Silica-induced gene 20 protein / SIG-20


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61255
#25: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61358
#26: Protein 60S ribosomal protein L27a / L29


Mass: 16648.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#27: Protein 60S ribosomal protein L29


Mass: 17635.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#28: Protein 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#29: Protein 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#30: Protein 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#31: Protein 60S ribosomal protein L35a


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#32: Protein 60S ribosomal protein L34


Mass: 13325.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#33: Protein 60S ribosomal protein L35


Mass: 14595.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#34: Protein 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWZ4
#35: Protein 60S ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#36: Protein 60S ribosomal protein L38


Mass: 8224.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8
#39: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947
#40: Protein 60S ribosomal protein L36a / 60S ribosomal protein L36a-like / 60S ribosomal protein L44


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P83882
#41: Protein 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61514
#42: Protein 60S ribosomal protein L28


Mass: 15770.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P41105

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Protein , 3 types, 3 molecules LlLmSg

#37: Protein Ribosomal protein L39-like


Mass: 6355.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQD0
#38: Protein Ubiquitin-60S ribosomal protein L40 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984
#67: Protein Receptor of activated protein C kinase 1 / 12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / ...12-3 / Guanine nucleotide-binding protein subunit beta-2-like 1 / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / p205


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68040

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Mus musculus ... , 4 types, 4 molecules L5L7L8S2

#43: RNA chain Mus musculus 28S ribosomal RNA


Mass: 1530907.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#44: RNA chain Mus musculus 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 396138
#45: RNA chain Mus musculus 5.8S ribosomal RNA


Mass: 50795.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1059793825
#46: RNA chain Mus musculus 18S ribosomal RNA


Mass: 603101.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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40S ribosomal protein ... , 30 types, 30 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSNSOSWSYSZSbSe

#47: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / ...37 kDa laminin receptor precursor / 37LRP / 37 kDa oncofetal antigen / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / OFA/iLRP


Mass: 32867.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14206
#48: Protein 40S ribosomal protein S3a / Protein TU-11


Mass: 29942.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97351
#49: Protein 40S ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P62908, DNA-(apurinic or apyrimidinic site) lyase
#50: Protein 40S ribosomal protein S4, X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62702
#51: Protein 40S ribosomal protein S5 / Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91V55
#52: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62082
#53: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62242
#54: Protein 40S ribosomal protein S10


Mass: 18951.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63325
#55: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62281
#56: Protein 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62843
#57: Protein 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14131
#58: Protein 40S ribosomal protein S17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63276
#59: Protein 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62270
#60: Protein 40S ribosomal protein S19


Mass: 16117.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZX8
#61: Protein 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P60867
#62: Protein 40S ribosomal protein S21


Mass: 9154.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQR2
#63: Protein 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62267
#64: Protein 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62855
#65: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62858
#66: Protein 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62274
#68: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25444
#69: Protein 40S ribosomal protein S6 / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62754
#70: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWN5
#71: Protein 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62301
#72: Protein 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62264
#73: Protein 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62245
#74: Protein 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62849
#75: Protein 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62852
#76: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWU9
#77: Protein 40S ribosomal protein S30


Mass: 14441.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q642K5

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RNA chain , 1 types, 1 molecules S6

#78: RNA chain Met-tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 269 molecules

#79: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 247 / Source method: obtained synthetically / Formula: Mg
#80: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#81: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mus musculus 80S ribosome from testis / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMTris-HCl1
2100 mMNaCl1
32 mMMgCl1
42 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100403 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 18.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097221332
ELECTRON MICROSCOPYf_angle_d0.8584325506
ELECTRON MICROSCOPYf_chiral_restr0.051340583
ELECTRON MICROSCOPYf_plane_restr0.005920632
ELECTRON MICROSCOPYf_dihedral_angle_d19.50478493

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