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- PDB-7qgg: Neuronal RNA granules are ribosome complexes stalled at the pre-t... -

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Basic information

Entry
Database: PDB / ID: 7qgg
TitleNeuronal RNA granules are ribosome complexes stalled at the pre-translocation state
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 38
  • (RNA (76-MER)) x 2
  • (Ribosomal protein ...) x 4
  • ALA-ALA-LYS-ALA
  • RNA (121-MER)
  • RNA (157-MER)
  • RNA (1872-MER)
  • RNA (4803-MER)
  • RNA (5'-D(P*()P*()P*()P*())-R(P*UP*UP*AP*CP*GP*GP*CP*GP*GP*UP*()P*()P*()P*()P*()P*())-3')
  • Receptor of activated protein C kinase 1
  • Rps16 protein
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-like domain-containing protein
KeywordsRIBOSOME / RNA granule / rat
Function / homology
Function and homology information


regulation of myeloid dendritic cell activation / : / positive regulation of selenocysteine incorporation / positive regulation of isoleucine-tRNA ligase activity / positive regulation of methionine-tRNA ligase activity / positive regulation of threonine-tRNA ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / mTORC1-mediated signalling ...regulation of myeloid dendritic cell activation / : / positive regulation of selenocysteine incorporation / positive regulation of isoleucine-tRNA ligase activity / positive regulation of methionine-tRNA ligase activity / positive regulation of threonine-tRNA ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / mTORC1-mediated signalling / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / CLEC7A (Dectin-1) signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Fanconi Anemia Pathway / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Cyclin D associated events in G1 / Stabilization of p53 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ER Quality Control Compartment (ERQC) / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / Inactivation of CSF3 (G-CSF) signaling / : / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOD1/2 Signaling Pathway / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / E3 ubiquitin ligases ubiquitinate target proteins / : / Translesion Synthesis by POLH / Downregulation of ERBB2:ERBB3 signaling / TCF dependent signaling in response to WNT / Regulation of innate immune responses to cytosolic DNA / HDR through Homologous Recombination (HRR) / Downregulation of ERBB2 signaling / Regulation of signaling by CBL / Downstream TCR signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / NOTCH3 Activation and Transmission of Signal to the Nucleus / Downregulation of ERBB4 signaling / Stimuli-sensing channels / Deactivation of the beta-catenin transactivating complex / Josephin domain DUBs / Ovarian tumor domain proteases / Negative regulation of MET activity / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Interleukin-1 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Regulation of PTEN localization / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / FCERI mediated NF-kB activation / Major pathway of rRNA processing in the nucleolus and cytosol / Pexophagy / cellular response to Thyroid stimulating hormone / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 5.8S rRNA binding / SCF-beta-TrCP mediated degradation of Emi1 / Metalloprotease DUBs / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Regulation of necroptotic cell death / Aggrephagy / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / metallochaperone-like domain / Ribosomal protein S12e / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L1, conserved site / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L1 signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L1 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL38 / Ribosomal protein L19 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL38 / Ribosomal protein L19 / Small ribosomal subunit protein uS14 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein uS19 / Ubiquitin-like domain-containing protein / Ribosomal protein L37 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / 60S ribosomal protein L37a / 40S ribosomal protein S25 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S27 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L27 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S5 / 60S ribosomal protein L34 / Large ribosomal subunit protein eL24 / 60S ribosomal protein L28 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS13 / Ribosomal protein L15 / 40S ribosomal protein S17 / 60S ribosomal protein L35a / 60S ribosomal protein L7 / 40S ribosomal protein S21 / 60S ribosomal protein L5 / 60S ribosomal protein L18 / 60S ribosomal protein L26 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S19 / 60S ribosomal protein L9 / 60S ribosomal protein L35 / 60S ribosomal protein L27a / 60S ribosomal protein L3 / 60S ribosomal protein L6 / 60S ribosomal protein L29 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 60S ribosomal protein L13 / 40S ribosomal protein S3a / 60S ribosomal protein L4 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 60S ribosomal protein L7a / 40S ribosomal protein S4, X isoform / 60S ribosomal protein L18a / 60S ribosomal protein L23a / 40S ribosomal protein S6 / 40S ribosomal protein S24 / 60S ribosomal protein L30 / 60S ribosomal protein L10a / 40S ribosomal protein S3 / 60S ribosomal protein L32 / 60S ribosomal protein L11 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S12 / 40S ribosomal protein S10 / 60S ribosomal protein L13a / Rps16 protein / 60S ribosomal protein L14 / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L10 / 60S ribosomal protein L22 / 60S ribosomal protein L21 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsPulk, A. / Kipper, K. / Mansour, A.
Funding support Estonia, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)IG 3911 Estonia
Estonian Research CouncilPSG87 Estonia
Estonian Research CouncilMOBTP44 Estonia
CitationJournal: J Mol Biol / Year: 2022
Title: Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state.
Authors: Kalle Kipper / Abbas Mansour / Arto Pulk /
Abstract: The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA- ...The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome-containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified a potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion.
History
DepositionDec 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S2: RNA (1872-MER)
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: Rps16 protein
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
SM: 40S ribosomal protein S12
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: Ubiquitin-like domain-containing protein
Sf: Ubiquitin-40S ribosomal protein S27a
A: 60S ribosomal protein L8
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4
D: RNA (157-MER)
E: RNA (121-MER)
F: 60S ribosomal protein L5
G: 60S ribosomal protein L6
H: 60S ribosomal protein L7
I: 60S ribosomal protein L7a
J: 60S ribosomal protein L9
K: 60S ribosomal protein L10
L: 60S ribosomal protein L11
M: 60S ribosomal protein L13
N: 60S ribosomal protein L14
O: Ribosomal protein L15
P: 60S ribosomal protein L13a
Q: 60S ribosomal protein L17
R: 60S ribosomal protein L18
S: Ribosomal protein L19
T: 60S ribosomal protein L18a
U: 60S ribosomal protein L21
V: 60S ribosomal protein L22
W: 60S ribosomal protein L23
X: 60S ribosomal protein L24
Y: 60S ribosomal protein L23a
Z: 60S ribosomal protein L26
a: 60S ribosomal protein L27
b: 60S ribosomal protein L27a
c: 60S ribosomal protein L29
d: 60S ribosomal protein L30
e: 60S ribosomal protein L31
f: 60S ribosomal protein L32
g: 60S ribosomal protein L35a
h: 60S ribosomal protein L34
i: 60S ribosomal protein L35
j: 60S ribosomal protein L36
k: Ribosomal protein L37
l: 60S ribosomal protein L38
m: 60S ribosomal protein L39
n: Ubiquitin-60S ribosomal protein L40
o: 60S ribosomal protein L41
p: Ribosomal protein L36a
q: 60S ribosomal protein L37a
r: 60S ribosomal protein L28
t: RNA (4803-MER)
u: RNA (76-MER)
v: RNA (76-MER)
w: RNA (5'-D(P*()P*()P*()P*())-R(P*UP*UP*AP*CP*GP*GP*CP*GP*GP*UP*()P*()P*()P*()P*()P*())-3')
Cz: 60S ribosomal protein L10a
y: ALA-ALA-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,778,137123
Polymers3,776,94284
Non-polymers1,19539
Water1448
1


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

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Components

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RNA chain , 7 types, 7 molecules S2DEtuvw

#1: RNA chain RNA (1872-MER)


Mass: 604241.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#38: RNA chain RNA (157-MER)


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 57148
#39: RNA chain RNA (121-MER)


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 793860
#79: RNA chain RNA (4803-MER)


Mass: 1553954.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#80: RNA chain RNA (76-MER)


Mass: 24414.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences. As the structure contains heterogeneous ...Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences. As the structure contains heterogeneous population of tRNAs then the identity of tRNA is unknown.
Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 1851728667
#81: RNA chain RNA (76-MER)


Mass: 24436.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences.As the structure contains heterogeneous ...Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences.As the structure contains heterogeneous population of tRNAs then the identity of tRNA is unknown.
Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 1879656365
#82: RNA chain RNA (5'-D(P*()P*()P*()P*())-R(P*UP*UP*AP*CP*GP*GP*CP*GP*GP*UP*()P*()P*()P*()P*()P*())-3')


Mass: 6360.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)

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40S ribosomal protein ... , 29 types, 29 molecules SASBSDSESFSHSISKSLSPSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSb

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


Mass: 32853.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P38983
#3: Protein 40S ribosomal protein S3a / V-fos transformation effector protein


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P49242
#4: Protein 40S ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P62909, DNA-(apurinic or apyrimidinic site) lyase
#5: Protein 40S ribosomal protein S4, X isoform


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62703
#6: Protein 40S ribosomal protein S5 / Ribosomal protein S5 / isoform CRA_b / Rps5 protein


Mass: 22943.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0BN81
#7: Protein 40S ribosomal protein S7 / S8


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62083
#8: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62243
#9: Protein 40S ribosomal protein S10


Mass: 18951.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63326
#10: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8B8VW69
#11: Protein 40S ribosomal protein S15


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K6QL61
#13: Protein 40S ribosomal protein S17


Mass: 15537.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P04644
#14: Protein 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: H0WTR0
#15: Protein 40S ribosomal protein S19


Mass: 16117.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P17074
#16: Protein 40S ribosomal protein S20


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P60868
#17: Protein 40S ribosomal protein S21


Mass: 9140.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P05765
#18: Protein 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A340WVW7
#19: Protein 40S ribosomal protein S26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K5LQY6
#20: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A3M0JHZ8
#21: Protein 40S ribosomal protein S29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2J8WKD7
#23: Protein 40S ribosomal protein S2


Mass: 31283.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P27952
#24: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62755
#25: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A6J0B498
#26: Protein 40S ribosomal protein S12


Mass: 14549.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63324
#27: Protein 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A663F1C0
#28: Protein 40S ribosomal protein S14


Mass: 16288.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P13471
#29: Protein 40S ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K5QKS6
#30: Protein 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62850
#31: Protein 40S ribosomal protein S25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A6J3IG71
#32: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A7J8BG50

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Protein , 5 types, 5 molecules SQSgSeSfn

#12: Protein Rps16 protein


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5XFV9
#22: Protein Receptor of activated protein C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K6K8B0
#33: Protein Ubiquitin-like domain-containing protein


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K6U587
#34: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 17990.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62982
#74: 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) Rattus norvegicus (Norway rat) / References: UniProt: Q6P7R7

+
60S ribosomal protein ... , 38 types, 38 molecules ABCFGHIJKLMNPQRTUVWXYZabcdefgh...

#35: Protein 60S ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8B8VPA8
#36: Protein 60S ribosomal protein L3 / L4


Mass: 46238.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P21531
#37: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1


Mass: 47363.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50878
#40: Protein 60S ribosomal protein L5


Mass: 34522.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P09895
#41: Protein 60S ribosomal protein L6 / Neoplasm-related protein C140


Mass: 33644.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P21533
#42: Protein 60S ribosomal protein L7


Mass: 30399.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P05426
#43: Protein 60S ribosomal protein L7a


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62425
#44: Protein 60S ribosomal protein L9


Mass: 21929.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P17077
#45: Protein 60S ribosomal protein L10 / Ribosomal protein L10


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PDV7
#46: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62914
#47: Protein 60S ribosomal protein L13


Mass: 24368.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P41123
#48: Protein 60S ribosomal protein L14


Mass: 23393.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q63507
#50: Protein 60S ribosomal protein L13a


Mass: 23501.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Please keep residue Gly 13 as it is. The Mass-spectrometry data shows that leading razor peptide for this protein is Uniprot Q5RK10.
Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5RK10
#51: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8J4KQ25
#52: Protein 60S ribosomal protein L18


Mass: 21712.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P12001
#54: Protein 60S ribosomal protein L18a


Mass: 20778.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62718
#55: Protein 60S ribosomal protein L21


Mass: 18624.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PDW2
#56: Protein 60S ribosomal protein L22 / RCG31311 / Ribosomal protein L22 / Ribosomal protein L22-like


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PDV8
#57: Protein 60S ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A3P9HH38
#58: Protein 60S ribosomal protein L24 / Ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F2X267
#59: Protein 60S ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62752
#60: Protein 60S ribosomal protein L26


Mass: 17322.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P12749
#61: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A851LWS6
#62: Protein 60S ribosomal protein L27a


Mass: 16661.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P18445
#63: Protein 60S ribosomal protein L29 / P23


Mass: 17374.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25886
#64: Protein 60S ribosomal protein L30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62890
#65: Protein 60S ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: G7NZE1
#66: Protein 60S ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62912
#67: Protein 60S ribosomal protein L35a


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P04646
#68: Protein 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B2RZD4
#69: Protein 60S ribosomal protein L35


Mass: 14595.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P17078
#70: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Please keep the Gly 49 as it is. Mass-spectrometry data indicates that leading razor peptide is D4A1Q0.
Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q9Y3U8
#72: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A1A7W9T9
#73: Protein 60S ribosomal protein L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A7N4PFJ2
#75: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62948
#77: Protein 60S ribosomal protein L37a / Ribosomal protein L37a


Mass: 10299.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A6J2LF66
#78: Protein 60S ribosomal protein L28


Mass: 15770.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F7EPV5
#83: Protein 60S ribosomal protein L10a


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62907

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Ribosomal protein ... , 4 types, 4 molecules OSkp

#49: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: L8Y0W1
#53: Protein Ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2J8KH59
#71: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2Y9RW09
#76: Protein Ribosomal protein L36a


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A7J7V6K8

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Protein/peptide , 1 types, 1 molecules y

#84: Protein/peptide ALA-ALA-LYS-ALA


Mass: 360.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)

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Non-polymers , 3 types, 47 molecules

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


Mass: 24.305 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Mg
#86: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#87: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Ribosome structure in the rat cortex-hippocampus derived neuronal RNA granules.
Type: COMPLEX / Entity ID: #1-#79, #82-#84 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Brain / Organelle: RNA granule / Tissue: Cortex and hippocampus
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMpotassium acetateKOAc1
34 mMmagnesium acetateMgOAc1
40.5 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 10 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3644

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20_4444refinement
PHENIX1.20_4444refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 499054
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62369 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6OLE

6ole


Accession code: 6OLE / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.49 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004234968
ELECTRON MICROSCOPYf_angle_d0.7387345320
ELECTRON MICROSCOPYf_chiral_restr0.035642991
ELECTRON MICROSCOPYf_plane_restr0.005822020
ELECTRON MICROSCOPYf_dihedral_angle_d14.78182916

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