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- PDB-9c3h: Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in ... -

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Basic information

Entry
Database: PDB / ID: 9c3h
TitleStructure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
Components
  • (Large ribosomal subunit protein ...) x 41
  • (Small ribosomal subunit protein ...) x 30
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • CCR4-NOT transcription complex subunit 3
  • FAU ubiquitin-like and ribosomal protein S30
  • Isoform 3 of Small ribosomal subunit protein eS24
  • Nascent chain
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • mRNA
  • tRNA-ARG,CCG-1
KeywordsRIBOSOME / mRNA degradation / CCR4-NOT complex / tRNA
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex ...CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / optic nerve development / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of formation of translation preinitiation complex / positive regulation of base-excision repair / regulation of translation involved in cellular response to UV / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / regulatory ncRNA-mediated gene silencing / positive regulation of Golgi to plasma membrane protein transport / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinal ganglion cell axon guidance / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / supercoiled DNA binding / neural crest cell differentiation / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of ubiquitin-protein transferase activity / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / middle ear morphogenesis / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / protein kinase A binding / pigmentation / Ribosomal scanning and start codon recognition / homeostatic process / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / monocyte chemotaxis / positive regulation of activated T cell proliferation / positive regulation of natural killer cell proliferation / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / blastocyst development / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process
Similarity search - Function
CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5 C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5 C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 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 L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L2, archaeal-type / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L19e, C-terminal domain / 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 S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / S27a-like superfamily / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal L18 C-terminal region / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / CCR4-NOT transcription complex subunit 3 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / CCR4-NOT transcription complex subunit 3 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / 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 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsErzberger, J.P. / Cruz, V.E.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA282036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RR150074 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220309 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
Welch FoundationI-1961 United States
Welch FoundationI-1897 United States
CitationJournal: Science / Year: 2024
Title: Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.
Authors: Xiaoqiang Zhu / Victor Emmanuel Cruz / He Zhang / Jan P Erzberger / Joshua T Mendell /
Abstract: The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. ...The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. Cryo-electron microscopy and transfer RNA (tRNA) mutagenesis demonstrated that the D-arms of select arginine tRNAs interact with CNOT3 and promote its recruitment whereas other tRNA D-arms sterically clash with CNOT3. These effects link codon content to mRNA stability. Thus, in addition to their canonical decoding function, tRNAs directly engage regulatory complexes during translation, a mechanism we term P-site tRNA-mediated mRNA decay.
History
DepositionJun 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L1: 5.8S rRNA
L5: 28S rRNA
L8: Large ribosomal subunit protein uL18
L9: 5S rRNA
LB: Large ribosomal subunit protein uL3
S4: tRNA-ARG,CCG-1
LC: Large ribosomal subunit protein uL4
LD: Large ribosomal subunit protein uL2
LE: Large ribosomal subunit protein uL24
LF: Large ribosomal subunit protein uL30
LG: Large ribosomal subunit protein eL8
LH: Large ribosomal subunit protein uL6
LI: Large ribosomal subunit protein eL32
LJ: Large ribosomal subunit protein uL5
LK: Large ribosomal subunit protein eL6
LM: Large ribosomal subunit protein eL14
LN: Large ribosomal subunit protein eL15
LO: Large ribosomal subunit protein uL29
LP: Large ribosomal subunit protein eL37
LQ: Large ribosomal subunit protein eL13
LR: Large ribosomal subunit protein eL19
LS: Large ribosomal subunit protein eL20
LT: Large ribosomal subunit protein eL21
LU: Large ribosomal subunit protein eL39
LV: Large ribosomal subunit protein uL14
LW: Large ribosomal subunit protein eL24
LY: Large ribosomal subunit protein uL13
LZ: Large ribosomal subunit protein eL27
La: Large ribosomal subunit protein uL15
Lb: Large ribosomal subunit protein eL29
Lc: Large ribosomal subunit protein eL30
Ld: Large ribosomal subunit protein eL31
Le: Large ribosomal subunit protein eL42
Lf: Large ribosomal subunit protein eL33
Lg: Large ribosomal subunit protein eL34
Lh: Large ribosomal subunit protein uL22
Li: Large ribosomal subunit protein eL36
Lj: Large ribosomal subunit protein eL18
Lk: Large ribosomal subunit protein eL38
Ll: Large ribosomal subunit protein eL28
Lm: Large ribosomal subunit protein eL22
Ln: Large ribosomal subunit protein uL23
Lo: Large ribosomal subunit protein eL40
Lp: Large ribosomal subunit protein eL43
Lz: Large ribosomal subunit protein uL16
NC: Nascent chain
S1: Small ribosomal subunit protein eS1
S2: 18S rRNA
S5: mRNA
SA: Small ribosomal subunit protein uS2
SB: CCR4-NOT transcription complex subunit 3
SC: Small ribosomal subunit protein uS5
SD: Small ribosomal subunit protein uS7
SE: Small ribosomal subunit protein eS4, X isoform
SG: Small ribosomal subunit protein eS6
SH: Small ribosomal subunit protein eS7
SI: Small ribosomal subunit protein eS8
SJ: Small ribosomal subunit protein uS4
SK: Small ribosomal subunit protein uS3
SL: Small ribosomal subunit protein uS17
SM: Small ribosomal subunit protein eS10
SN: Small ribosomal subunit protein uS15
SO: Small ribosomal subunit protein uS11
SP: Small ribosomal subunit protein uS19
SQ: Small ribosomal subunit protein uS9
SS: Small ribosomal subunit protein eS17
ST: Small ribosomal subunit protein uS13
SU: Small ribosomal subunit protein eS19
SV: Small ribosomal subunit protein eS21
SW: Small ribosomal subunit protein uS8
SX: Small ribosomal subunit protein uS12
SY: Isoform 3 of Small ribosomal subunit protein eS24
SZ: Small ribosomal subunit protein uS10
Sa: Small ribosomal subunit protein eS26
Sb: Small ribosomal subunit protein eS27
Sc: Small ribosomal subunit protein eS25
Sd: Small ribosomal subunit protein eS28
Se: FAU ubiquitin-like and ribosomal protein S30
Sf: Small ribosomal subunit protein uS14
Sg: Receptor of activated protein C kinase 1
So: Small ribosomal subunit protein eS32
Sy: Small ribosomal subunit protein eS12
Sz: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,893,391512
Polymers3,880,98783
Non-polymers12,404429
Water170,8729485
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules L1L5L9S4S2S5

#1: RNA chain 5.8S rRNA


Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#2: RNA chain 28S rRNA


Mass: 1640938.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: RNA chain 5S rRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#6: RNA chain tRNA-ARG,CCG-1


Mass: 24661.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#48: RNA chain 18S rRNA


Mass: 603582.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#49: RNA chain mRNA


Mass: 2847.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

#3: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#5: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B


Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#7: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4 / 60S ribosomal protein L1


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#8: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#9: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#10: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 29306.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#11: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#12: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#13: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#14: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11 / CLL-associated antigen KW-12


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#15: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#16: Protein Large ribosomal subunit protein eL14 / 60S ribosomal protein L14 / CAG-ISL 7


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#17: Protein Large ribosomal subunit protein eL15 / 60S ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#18: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#19: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#20: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#21: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#22: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#23: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#24: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#25: Protein Large ribosomal subunit protein uL14 / 60S ribosomal protein L23 / 60S ribosomal protein L17


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#26: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24 / 60S ribosomal protein L30


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#27: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / 23 kDa highly basic protein


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#28: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#29: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a


Mass: 16619.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#30: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP


Mass: 17817.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#31: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#32: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#33: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / ...60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#34: Protein Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#35: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#36: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17 / 60S ribosomal protein L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#37: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#38: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#39: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#40: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15679.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#41: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated ...60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#42: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#43: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40


Mass: 11512.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#45: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor ...60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635

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Protein/peptide , 1 types, 1 molecules NC

#46: Protein/peptide Nascent chain


Mass: 3258.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

#47: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#50: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4


Mass: 32778.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#52: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#53: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#54: Protein Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#55: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6 / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#56: Protein Small ribosomal subunit protein eS7 / 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#57: Protein Small ribosomal subunit protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#58: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#59: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#60: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#61: Protein Small ribosomal subunit protein eS10 / 40S ribosomal protein S10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#62: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#63: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#64: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#65: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#66: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#67: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#68: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#69: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#70: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#71: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#73: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#74: Protein Small ribosomal subunit protein eS26 / 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#75: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#76: Protein Small ribosomal subunit protein eS25 / 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#77: Protein Small ribosomal subunit protein eS28 / 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#79: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#81: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#82: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398

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Protein , 5 types, 5 molecules SBSYSeSgSz

#51: Protein CCR4-NOT transcription complex subunit 3 / CCR4-associated factor 3 / Leukocyte receptor cluster member 2


Mass: 64125.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75175
#72: Protein Isoform 3 of Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#78: Protein FAU ubiquitin-like and ribosomal protein S30


Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#80: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#83: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

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Non-polymers , 5 types, 9914 molecules

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


Mass: 24.305 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: Mg
#85: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: K
#86: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#88: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9485 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 80S ribosome in complex with CNOT3 and P-site tRNA ARG CCG-1
Type: RIBOSOME / Entity ID: #1-#54, #56-#83 / Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 1900 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 17 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276000 / Symmetry type: POINT

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