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- PDB-6g5i: Cryo-EM structure of a late human pre-40S ribosomal subunit - State R -

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Basic information

Entry
Database: PDB / ID: 6g5i
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State R
Components
  • (40S ribosomal protein ...) x 30
  • (RNA-binding protein ...) x 2
  • 18S ribosomal RNA
  • Receptor of activated protein C kinase 1
  • Ribosomal protein S27aRibosome
  • Serine/threonine-protein kinase RIO1
KeywordsRIBOSOME / 40S / pre-40S / ribosome biogenesis
Function / homology
Function and homology information


methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / cleavage involved in rRNA processing / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport ...methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / cleavage involved in rRNA processing / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / IRE1-RACK1-PP2A complex / negative regulation of RNA splicing / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / TNFR1-mediated ceramide production / regulation of cell division / cytoplasmic side of rough endoplasmic reticulum membrane / rRNA modification in the nucleus and cytosol / laminin receptor activity / 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 / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of phagocytosis / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / NF-kappaB complex / regulation of establishment of cell polarity / Ribosomal scanning and start codon recognition / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / positive regulation of endodeoxyribonuclease activity / Translation initiation complex formation / oxidized purine DNA binding / positive regulation of mitochondrial depolarization / translation regulator activity / supercoiled DNA binding / ion channel inhibitor activity / preribosome, small subunit precursor / phagocytic cup / positive regulation of apoptotic signaling pathway / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase A binding / negative regulation of smoothened signaling pathway / TOR signaling / erythrocyte development / iron-sulfur cluster binding / ubiquitin-like protein conjugating enzyme binding / Peptide chain elongation / positive regulation of cellular component movement / fibroblast growth factor binding / Selenocysteine synthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / mTORC1-mediated signalling / rescue of stalled ribosome / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / poly(U) RNA binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / monocyte chemotaxis / T cell proliferation involved in immune response / stress granule assembly / BH3 domain binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / DNA-(apurinic or apyrimidinic site) lyase / Viral mRNA Translation / 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) / GABA-ergic synapse / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of activated T cell proliferation / positive regulation of T cell receptor signaling pathway / ribosomal small subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of translational fidelity / maturation of SSU-rRNA / regulation of tumor necrosis factor-mediated signaling pathway / Protein methylation / gastrulation / negative regulation of respiratory burst involved in inflammatory response / MDM2/MDM4 family protein binding / negative regulation of protein kinase B signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / spindle assembly
Similarity search - Function
Serine/threonine-protein kinase Rio1 / Putative WW-binding domain and destruction box / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon like / NOB1 zinc finger-like superfamily / Nin one binding (NOB1) Zn-ribbon-like / Ribonuclease Nob1, eukaryote / Ribonuclease, PIN domain / PIN domain of ribonuclease / RNA-binding protein NOB1 ...Serine/threonine-protein kinase Rio1 / Putative WW-binding domain and destruction box / Putative WW-binding domain and destruction box / Nin one binding (NOB1) Zn-ribbon like / NOB1 zinc finger-like superfamily / Nin one binding (NOB1) Zn-ribbon-like / Ribonuclease Nob1, eukaryote / Ribonuclease, PIN domain / PIN domain of ribonuclease / RNA-binding protein NOB1 / Ribosomal protein S8e, subdomain / Ribosomal protein S4, central domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase, conserved site / RIO1 family / RIO kinase / RIO-like kinase / Pre-rRNA-processing protein PNO1-like / Large family of predicted nucleotide-binding domains / PIN domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S11/S14 / Dna Ligase; domain 1 - #10 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / 40S ribosomal protein SA / S15/NS1, RNA-binding / 40S ribosomal protein SA C-terminus / 40S ribosomal protein SA, C-terminal domain / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Double Stranded RNA Binding Domain - #20 / Ribosomal protein S8e subdomain, eukaryotes / K Homology domain, type 1 superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal protein S21e signature. / Ribosomal protein S21e, conserved site / Ribosomal Protein S5; domain 2 - #10 / Ribosomal protein S21e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S2, eukaryotic / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / N-terminal domain of TfIIb / 40S Ribosomal protein S10 / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S10, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein S25 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal_S19e / : / Ribosomal protein S19e / Ribosomal protein S19e / Plectin/S10, N-terminal / Plectin/S10 domain / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S17e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal S17 / Ribosomal protein S17e-like superfamily / Ribosomal protein S27e signature. / Ribosomal protein S7e signature. / RS4NT (NUC023) domain / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4e, central region / Ribosomal family S4e / Ribosomal protein S4, KOW domain / Ribosomal protein S6, eukaryotic / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S24e signature.
Similarity search - Domain/homology
RNA (> 1000) / 40S ribosomal protein S24 / 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 S15 / 40S ribosomal protein S30 ...RNA (> 1000) / 40S ribosomal protein S24 / 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 S15 / 40S ribosomal protein S30 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / 40S ribosomal protein S14 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S27a / Serine/threonine-protein kinase RIO1 / RNA-binding protein PNO1 / 40S ribosomal protein S23 / 40S ribosomal protein S15a / 40S ribosomal protein S16 / 40S ribosomal protein S12 / RNA (> 10) / RNA / : / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S19 / RNA (> 100) / 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 / 40S ribosomal protein S8 / RNA-binding protein NOB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAmeismeier, M. / Cheng, J. / Berninghausen, O. / Beckmann, R.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB646 Germany
German Research FoundationGRK1721 Germany
German Research FoundationFOR1805 Germany
European Research CouncilCRYOTRANSLATION Germany
CitationJournal: Nature / Year: 2018
Title: Visualizing late states of human 40S ribosomal subunit maturation.
Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann /
Abstract: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
2: 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: Ribosomal protein S27a
g: Receptor of activated protein C kinase 1
x: RNA-binding protein PNO1
y: RNA-binding protein NOB1
z: Serine/threonine-protein kinase RIO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,353,76139
Polymers1,353,56536
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area201350 Å2
ΔGint-1440 kcal/mol
Surface area417600 Å2
MethodPISA

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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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293
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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / References: UniProt: P62861

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Protein , 3 types, 3 molecules fgz

#32: Protein Ribosomal protein S27a / Ribosome


Mass: 17944.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q5RKT7, UniProt: P62979*PLUS
#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) / Cell line: HEK293 / References: UniProt: P63244
#36: Protein Serine/threonine-protein kinase RIO1 / RIO kinase 1


Mass: 65692.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK1 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q9BRS2, non-specific serine/threonine protein kinase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNO1 / Production host: Escherichia coli K-12 (bacteria) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOB1, ART4, NOB1P, PSMD8BP1, MSTP158 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9ULX3

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

#1: RNA chain 18S ribosomal RNA /


Mass: 607057.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: GenBank: 151415227
#37: Chemical ChemComp-ZN / ZINC ION / Zinc


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

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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: Cryo-EM structure of a late human pre-40S ribosomal subunit - State R
Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83883 / Symmetry type: POINT

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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