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- PDB-6zuo: Human RIO1(kd)-StHA late pre-40S particle, structural state A (pr... -

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Basic information

Entry
Database: PDB / ID: 6zuo
TitleHuman RIO1(kd)-StHA late pre-40S particle, structural state A (pre 18S rRNA cleavage)
Components
  • (40S ribosomal protein ...) x 30
  • (RNA-binding protein ...) x 2
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • pre-18S ribosomal RNA
KeywordsRIBOSOME / Human ribosome biogenesis / small ribosomal subunit / rRNA processing
Function / homology
Function and homology information


cleavage involved in rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / mammalian oogenesis stage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex ...cleavage involved in rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / mammalian oogenesis stage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / cytoplasmic side of rough endoplasmic reticulum membrane / TNFR1-mediated ceramide production / laminin receptor activity / rRNA modification in the nucleus and cytosol / regulation of cell division / activation-induced cell death of T cells / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / negative regulation of ubiquitin protein ligase activity / positive regulation of ceramide biosynthetic process / positive regulation of base-excision repair / oxidized pyrimidine DNA binding / positive regulation of DNA N-glycosylase activity / response to TNF agonist / negative regulation of DNA repair / erythrocyte homeostasis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of phagocytosis / NF-kappaB complex / regulation of establishment of cell polarity / signaling adaptor activity / negative regulation of Wnt signaling pathway / positive regulation of endodeoxyribonuclease activity / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of mitochondrial depolarization / translation regulator activity / supercoiled DNA binding / protein kinase A binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phagocytic cup / ion channel inhibitor activity / preribosome, small subunit precursor / positive regulation of apoptotic signaling pathway / negative regulation of smoothened signaling pathway / erythrocyte development / TOR signaling / iron-sulfur cluster binding / ubiquitin-like protein conjugating enzyme binding / Peptide chain elongation / Ribosomal scanning and start codon recognition / positive regulation of cellular component movement / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / fibroblast growth factor binding / Selenocysteine synthesis / rescue of stalled ribosome / mTORC1-mediated signalling / Formation of a pool of free 40S subunits / Translation initiation complex formation / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / T cell proliferation involved in immune response / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / Viral mRNA Translation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of cyclic-nucleotide phosphodiesterase activity / GABA-ergic synapse / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of T cell receptor signaling pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / maturation of SSU-rRNA / regulation of tumor necrosis factor-mediated signaling pathway / regulation of translational fidelity / Protein methylation / gastrulation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / spindle assembly / small-subunit processome / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase
Similarity search - Function
NOB1 zinc finger-like superfamily / Ribonuclease Nob1, eukaryote / Nin one binding (NOB1) Zn-ribbon like / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon-like / Putative WW-binding domain and destruction box / Ribonuclease, PIN domain / RNA-binding protein NOB1 / PIN domain of ribonuclease / Pre-rRNA-processing protein PNO1-like ...NOB1 zinc finger-like superfamily / Ribonuclease Nob1, eukaryote / Nin one binding (NOB1) Zn-ribbon like / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon-like / Putative WW-binding domain and destruction box / Ribonuclease, PIN domain / RNA-binding protein NOB1 / PIN domain of ribonuclease / Pre-rRNA-processing protein PNO1-like / Large family of predicted nucleotide-binding domains / PIN domain / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein S8e subdomain, eukaryotes / K Homology domain, type 1 superfamily / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein S12e signature. / Ribosomal protein S19e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S12e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S25 / S25 ribosomal protein / Plectin/S10 domain / Plectin/S10, N-terminal / : / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S17e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e signature. / Ribosomal protein S17e-like superfamily / Ribosomal protein S17e / Ribosomal S17 / Ribosomal protein S27e signature. / Ribosomal protein S7e signature. / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / Ribosomal family S4e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4e, central region / Ribosomal protein S24e / Ribosomal protein S6, eukaryotic / Ribosomal protein S24e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S23, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S6e, conserved site / Ribosomal protein S6e signature. / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S3Ae / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S15P / Ribosomal protein S28e conserved site / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S28e signature. / Ribosomal protein S13/S15, N-terminal / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S28e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein S4/S9, eukaryotic/archaeal
Similarity search - Domain/homology
40S ribosomal protein S15 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S28 / 40S ribosomal protein S24 ...40S ribosomal protein S15 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S28 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S21 / 40S ribosomal protein S30 / Ubiquitin-40S ribosomal protein S27a / RNA-binding protein PNO1 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S16 / 40S ribosomal protein S14 / RNA (> 1000) / 40S ribosomal protein S15a / 40S ribosomal protein S12 / RNA (> 10) / RNA / RNA (> 100) / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S19 / 40S ribosomal protein S8 / 40S ribosomal protein S27 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / RNA-binding protein NOB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPlassart, L. / Shayan, R. / Plisson-Chastang, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR 16-CE11-0029 France
CitationJournal: Elife / Year: 2021
Title: The final step of 40S ribosomal subunit maturation is controlled by a dual key lock.
Authors: Laura Plassart / Ramtin Shayan / Christian Montellese / Dana Rinaldi / Natacha Larburu / Carole Pichereaux / Carine Froment / Simon Lebaron / Marie-Françoise O'Donohue / Ulrike Kutay / ...Authors: Laura Plassart / Ramtin Shayan / Christian Montellese / Dana Rinaldi / Natacha Larburu / Carole Pichereaux / Carine Froment / Simon Lebaron / Marie-Françoise O'Donohue / Ulrike Kutay / Julien Marcoux / Pierre-Emmanuel Gleizes / Celia Plisson-Chastang /
Abstract: Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, ...Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
2: pre-18S ribosomal RNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
D: 40S ribosomal protein S3
E: 40S ribosomal protein S4, X isoform
F: 40S ribosomal protein S5
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
K: 40S ribosomal protein S10
L: 40S ribosomal protein S11
M: 40S ribosomal protein S12
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
R: 40S ribosomal protein S17
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
U: 40S ribosomal protein S20
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
Z: 40S ribosomal protein S25
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ubiquitin-40S ribosomal protein S27a
g: Receptor of activated protein C kinase 1
x: RNA-binding protein PNO1
y: RNA-binding protein NOB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,284,17838
Polymers1,283,98235
Non-polymers1963
Water0
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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40S ribosomal protein ... , 30 types, 30 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZbcde

#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 / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#3: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / 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
#4: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#5: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


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
#6: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#7: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#8: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


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


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


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


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#12: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#13: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#14: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#15: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


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


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


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


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


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


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


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#22: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#23: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


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


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


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#26: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#27: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#28: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#29: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


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


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#31: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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Protein , 2 types, 2 molecules fg

#32: 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
#33: 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

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RNA-binding protein ... , 2 types, 2 molecules xy

#34: Protein RNA-binding protein PNO1


Mass: 27970.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX1
#35: Protein RNA-binding protein NOB1 / Phosphorylation regulatory protein HP-10 / Protein ART-4


Mass: 46743.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9ULX3, Hydrolases; Acting on ester bonds

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RNA chain / Non-polymers , 2 types, 4 molecules 2

#1: RNA chain pre-18S ribosomal RNA


Mass: 603107.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293
#36: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human cytoplasmic late precursor to the small ribosomal subunit, purified using RIO1(kd)-StHA as bait. Structural state A (pre 18S rRNA maturation)
Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK 293
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 29.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9494
Image scansMovie frames/image: 28

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2Seriimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELION3.0.4initial Euler assignment
10RELION3.0.4final Euler assignment
11RELIONclassification
12RELION3D reconstruction
13REFMACmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2126610
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104844 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6G51
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00882008
ELECTRON MICROSCOPYf_angle_d1.067118686
ELECTRON MICROSCOPYf_dihedral_angle_d14.00146076
ELECTRON MICROSCOPYf_chiral_restr0.05714646
ELECTRON MICROSCOPYf_plane_restr0.0078879

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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