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- PDB-9h4n: RPL13 (eL13)-mutant 80S ribosome from mouse -

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Basic information

Entry
Database: PDB / ID: 9h4n
TitleRPL13 (eL13)-mutant 80S ribosome from mouse
Components
  • (40S ribosomal protein ...) x 7
  • (60S ribosomal protein ...) x 10
  • (Large ribosomal subunit protein ...) x 31
  • (Small ribosomal subunit protein ...) x 21
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Messenger RNA
  • Receptor of activated protein C kinase 1
  • Transfer RNA
KeywordsRIBOSOME / Mouse liver 80S ribosome / Spondyloepimetaphyseal dysplasia / RPL13 (eL13) mutation
Function / homology
Function and homology information


5.8S rRNA binding / Protein hydroxylation / 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 ...5.8S rRNA binding / Protein hydroxylation / 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 / 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 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / 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 / 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 / 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 / DNA Damage Recognition in GG-NER / 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 / 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 / TNFR1-induced NF-kappa-B signaling pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Inactivation of CSF3 (G-CSF) signaling / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / translation at postsynapse / Autodegradation of the E3 ubiquitin ligase COP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Protein methylation / Regulation of TNFR1 signaling / Asymmetric localization of PCP proteins
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / 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 L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein 60S L18 and 50S L18e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / 60S ribosomal protein L35 / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / : / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / 60S ribosomal protein L19 / Ribosomal protein S19e / Ribosomal protein L34Ae
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / 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 eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / 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 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / 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 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL16-like / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein eS27-like / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / 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: 2.46 Å
AuthorsOrgebin, E. / Astier, A. / Rinaldi, D. / Baud'huin, M. / Plisson-Chastang, C.
Funding support France, 1items
OrganizationGrant numberCountry
Institut National du Cancer (inCA) France
CitationJournal: To Be Published
Title: Analysis of Rpl13 variant consequences on bone development using a mouse model of spondyloepimetaphyseal dysplasia (Isidor-Toutain type)
Authors: Orgebin, E. / Astier, A. / Rinaldi, D. / Lamoureux, F. / Georges, S. / Brounais-Le Royer, B. / Charrier, C. / Amiaud, J. / Battaglia, S. / Kenis, V. / Markova, T. / Tsabai, P. / Tuttle, A. / ...Authors: Orgebin, E. / Astier, A. / Rinaldi, D. / Lamoureux, F. / Georges, S. / Brounais-Le Royer, B. / Charrier, C. / Amiaud, J. / Battaglia, S. / Kenis, V. / Markova, T. / Tsabai, P. / Tuttle, A. / Grand, K. / Sanchez, P. / Gleizes, P.E. / Vincent, M. / Isidor, B. / Verrechia, F. / Ory, B. / Plisson-Chastang, C. / Lezot, F. / Baud'huin, M.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A1: Large ribosomal subunit protein uL30
B1: Large ribosomal subunit protein eL8
C1: Large ribosomal subunit protein uL6
D1: Large ribosomal subunit protein uL16-like
E1: Large ribosomal subunit protein uL5
F1: Large ribosomal subunit protein eL13
G1: 60S ribosomal protein L14
H1: 60S ribosomal protein L15
A2: 28S ribosomal RNA
B2: 5S ribosomal RNA
C2: 5.8S ribosomal RNA
D2: Large ribosomal subunit protein uL2
E2: Large ribosomal subunit protein uL3
F2: Large ribosomal subunit protein uL4
G2: Large ribosomal subunit protein uL18
H2: 60S ribosomal protein L6
I2: Large ribosomal subunit protein uL13
J2: 60S ribosomal protein L17
K2: Large ribosomal subunit protein eL18
L2: Large ribosomal subunit protein eL19
M2: Large ribosomal subunit protein eL20
N2: Large ribosomal subunit protein eL21
O2: Large ribosomal subunit protein eL22
P2: 60S ribosomal protein L23
Q2: Large ribosomal subunit protein eL24
R2: 60S ribosomal protein L23a
S2: Large ribosomal subunit protein uL24
T2: Large ribosomal subunit protein eL27
U2: 60S ribosomal protein L27a
V2: Large ribosomal subunit protein eL29
W2: Large ribosomal subunit protein eL30
X2: Large ribosomal subunit protein eL31
Y2: Large ribosomal subunit protein eL32
Z2: 60S ribosomal protein L35a
a2: 60S ribosomal protein L34
b2: Large ribosomal subunit protein uL29
c2: Large ribosomal subunit protein eL36
d2: Large ribosomal subunit protein eL37
e2: 60S ribosomal protein L38
f2: Large ribosomal subunit protein eL39
g2: Large ribosomal subunit protein eL40
h2: Small ribosomal subunit protein eS32
i2: Large ribosomal subunit protein eL42
j2: Large ribosomal subunit protein eL43
k2: Large ribosomal subunit protein eL28
m2: 18S ribosomal RNA
n2: Transfer RNA
p2: Small ribosomal subunit protein eS1
q2: Small ribosomal subunit protein uS3
r2: Small ribosomal subunit protein eS4
w2: Small ribosomal subunit protein uS17
z2: 40S ribosomal protein S17
o2: Small ribosomal subunit protein uS2
s2: 40S ribosomal protein S5
v2: 40S ribosomal protein S10
x2: Small ribosomal subunit protein uS19
y2: Small ribosomal subunit protein uS9
A3: Small ribosomal subunit protein uS13
B3: Small ribosomal subunit protein eS19
C3: 40S ribosomal protein S20
D3: Small ribosomal subunit protein eS21
E3: Small ribosomal subunit protein uS12
G3: 40S ribosomal protein S28
H3: Small ribosomal subunit protein uS14
I3: Receptor of activated protein C kinase 1
J3: Small ribosomal subunit protein uS5
K3: 40S ribosomal protein S6
L3: Small ribosomal subunit protein uS4
N3: Small ribosomal subunit protein uS15
P3: Small ribosomal subunit protein uS8
Q3: Small ribosomal subunit protein eS24
S3: Small ribosomal subunit protein eS27-like
T3: 40S ribosomal protein S30
Bx: Messenger RNA
F3: Small ribosomal subunit protein eS26
O3: Small ribosomal subunit protein uS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,015,95783
Polymers3,015,54076
Non-polymers4177
Water724
1


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

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Components

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Large ribosomal subunit protein ... , 31 types, 31 molecules A1B1C1D1E1F1D2E2F2G2I2K2L2M2N2O2Q2S2T2V2W2X2Y2b2c2d2f2g2i2j2k2

#1: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 26199.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 60S ribosomal protein L7 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#2: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 26491.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#3: Protein Large ribosomal subunit protein uL6 / 60S ribosomal protein L9


Mass: 21673.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#4: Protein Large ribosomal subunit protein uL16-like / 60S ribosomal protein L10-like


Mass: 24480.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P86048
#5: Protein Large ribosomal subunit protein uL5 / 60S ribosomal protein L11


Mass: 19899.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#6: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / A52


Mass: 23374.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#12: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 27328.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#13: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / J1 protein


Mass: 46080.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#14: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 40891.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#15: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34046.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#17: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 23317.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#19: Protein Large ribosomal subunit protein eL18 / 60S ribosomal protein L18


Mass: 21510.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#20: Protein Large ribosomal subunit protein eL19 / 60S ribosomal protein L19


Mass: 19595.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#21: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20647.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#22: Protein Large ribosomal subunit protein eL21 / 60S ribosomal protein L21


Mass: 18492.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09167
#23: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / Heparin-binding protein HBp15


Mass: 11722.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#25: Protein Large ribosomal subunit protein eL24 / 60S ribosomal protein L24


Mass: 7384.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#27: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26 / Silica-induced gene 20 protein / SIG-20


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61255
#28: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61358
#30: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29


Mass: 13500.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#31: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 10496.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#32: Protein Large ribosomal subunit protein eL31 / 60S ribosomal protein L31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#33: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#36: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14264.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#37: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 11915.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47964
#38: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#40: Protein/peptide Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62892
#41: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40 / CEP52


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62984
#43: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44


Mass: 12070.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P83882
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 9967.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P61514
#45: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 14306.797 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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60S ribosomal protein ... , 10 types, 10 molecules G1H1H2J2P2R2U2Z2a2e2

#7: Protein 60S ribosomal protein L14


Mass: 16301.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#8: Protein 60S ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#16: Protein 60S ribosomal protein L6


Mass: 25410.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#18: Protein 60S ribosomal protein L17


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR4
#24: Protein 60S ribosomal protein L23


Mass: 13828.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#26: Protein 60S ribosomal protein L23a


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#29: Protein 60S ribosomal protein L27a / L29


Mass: 16517.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#34: Protein 60S ribosomal protein L35a


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#35: Protein 60S ribosomal protein L34


Mass: 12993.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#39: Protein 60S ribosomal protein L38


Mass: 8093.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8

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RNA chain , 6 types, 6 molecules A2B2C2m2n2Bx

#9: RNA chain 28S ribosomal RNA


Mass: 1169498.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#10: RNA chain 5S ribosomal RNA


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


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1756494520
#46: RNA chain 18S ribosomal RNA


Mass: 556356.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#47: RNA chain Transfer RNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 174924
#74: RNA chain Messenger RNA


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Small ribosomal subunit protein ... , 21 types, 21 molecules h2p2q2r2w2o2x2y2A3B3D3E3H3J3L3N3P3Q3S3F3O3

#42: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41


Mass: 3344.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947
#48: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / Protein TU-11


Mass: 24888.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97351
#49: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 25027.340 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 Small ribosomal subunit protein eS4 / 40S ribosomal protein S4 / X isoform


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62702
#51: Protein Small ribosomal subunit protein uS17 / 40S ribosomal protein S11


Mass: 17785.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62281
#53: Protein Small ribosomal subunit protein uS2 / 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 / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / OFA/iLRP


Mass: 24102.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14206
#56: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 15328.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62843
#57: Protein Small ribosomal subunit protein uS9 / 40S ribosomal protein S16


Mass: 16249.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14131
#58: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


Mass: 16898.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62270
#59: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 15694.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZX8
#61: Protein Small ribosomal subunit protein eS21 / 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
#62: Protein Small ribosomal subunit protein uS12 / 40S ribosomal protein S23


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62267
#64: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29


Mass: 6502.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62274
#66: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3


Mass: 24568.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25444
#68: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWN5
#69: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62301
#70: Protein Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62245
#71: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 14976.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62849
#72: Protein Small ribosomal subunit protein eS27-like / 40S ribosomal protein S27-like


Mass: 9365.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWY3
#75: Protein Small ribosomal subunit protein eS26 / 40S ribosomal protein S26


Mass: 11087.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62855
#76: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 14231.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62264

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40S ribosomal protein ... , 7 types, 7 molecules z2s2v2C3G3K3T3

#52: Protein 40S ribosomal protein S17


Mass: 12481.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#54: Protein 40S ribosomal protein S5


Mass: 15981.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#55: Protein 40S ribosomal protein S10


Mass: 6956.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#60: Protein/peptide 40S ribosomal protein S20


Mass: 1758.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#63: Protein/peptide 40S ribosomal protein S28


Mass: 735.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#67: Protein 40S ribosomal protein S6


Mass: 21724.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#73: Protein/peptide 40S ribosomal protein S30


Mass: 4682.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein , 1 types, 1 molecules I3

#65: Protein Receptor of activated protein C kinase 1


Mass: 18759.055 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, 11 molecules

#77: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#78: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#79: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: RPL13 (eL13)-mutant 80S ribosome from mouse / Type: RIBOSOME / Entity ID: #1-#76 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepes potassium hydroxydeHepes-KOH1
250 mMPotassium chlorideKCl1
310 mMSodium chlorideNaCl1
410 mMMagnesium chlorideMgCl21
51 mMDithiothreitolDTT1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 292 K / Details: 1,2 second blotting

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1RELION4particle selectionTopaz
4CTFFIND4.1CTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 801375
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235429 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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