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- EMDB-4351: Cryo-EM structure of a late human pre-40S ribosomal subunit - State E -

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Basic information

Entry
Database: EMDB / ID: EMD-4351
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State E
Map data
SampleCryo-EM structure of a late human pre-40S ribosomal subunit - State E
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 30
  • (RNA-binding protein ...) x 2
  • Pre-rRNA-processing protein TSR1 homolog
  • Protein LTV1 homolog
  • Ubiquitin-40S ribosomal protein S27a
  • Receptor of activated protein C kinase 1
Function / homology
Function and homology information


cleavage involved in rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of DNA repair / response to TNF agonist / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization ...cleavage involved in rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of DNA repair / response to TNF agonist / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / ubiquitin ligase inhibitor activity / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / regulation of cell division / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / U3 snoRNA binding / signaling adaptor activity / negative regulation of ubiquitin protein ligase activity / negative regulation of endoplasmic reticulum unfolded protein response / erythrocyte homeostasis / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / ubiquitin-like protein conjugating enzyme binding / positive regulation of ceramide biosynthetic process / negative regulation of phagocytosis / negative regulation of Wnt signaling pathway / regulation of establishment of cell polarity / pigmentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell receptor signaling pathway / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / positive regulation of mitochondrial depolarization / preribosome, small subunit precursor / phagocytic cup / rescue of stalled ribosome / positive regulation of activated T cell proliferation / ion channel inhibitor activity / positive regulation of cellular component movement / iron-sulfur cluster binding / fibroblast growth factor 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) / stress granule assembly / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / poly(U) RNA binding / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / regulation of translational fidelity / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / monocyte chemotaxis / positive regulation of ubiquitin-protein transferase activity / positive regulation of interleukin-2 production / spindle assembly / BH3 domain binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / ribosomal small subunit export from nucleus / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / TOR signaling / negative regulation of protein kinase B signaling / positive regulation of JUN kinase activity / regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / gastrulation / viral transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ribosomal small subunit biogenesis / negative regulation of respiratory burst involved in inflammatory response / polysome / positive regulation of microtubule polymerization / molecular adaptor activity / translation initiation factor binding / positive regulation of DNA repair / innate immune response in mucosa / laminin binding / Hsp70 protein binding / erythrocyte differentiation / translational initiation / polysomal ribosome / tubulin binding / positive regulation of cell cycle / endodeoxyribonuclease activity / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of peptidyl-serine phosphorylation / visual perception / negative regulation of protein ubiquitination / mRNA 3'-UTR binding / positive regulation of translational fidelity / small ribosomal subunit rRNA binding
Ribosomal protein S21e, conserved site / RNA-binding S4 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 ...Ribosomal protein S21e, conserved site / RNA-binding S4 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S2, eukaryotic / Ribosomal protein S24e / 40S ribosomal protein S1/3, eukaryotes / DNA methylase, N-6 adenine-specific, conserved site / Ribosomal protein S19/S15 / PIN domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S3Ae / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Bms1/Tsr1-type G domain / 50S ribosomal protein L30e-like / Ribosomal protein S3, eukaryotic/archaeal / S-adenosyl-L-methionine-dependent methyltransferase / K Homology domain, type 2 / Ribosomal protein S28e conserved site / Plectin/S10, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S25 / K Homology domain / 40S ribosomal protein SA / WD40 repeat / Ribosomal protein S6e / Ribosomal protein S19A/S15e / Ribosomal protein S2, flavodoxin-like domain superfamily / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S6e, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S5/S7 / Ribosomal protein S3, C-terminal / Ribosomal protein S9 / Ribosomal protein S19e / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S5 / Ribosomal protein S8 / Ribosomal protein S7 domain / Ribosomal protein S27e / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S12e / Ribosomal protein S28e / Ribosomal protein S17/S11 / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S5/S7, eukaryotic/archaeal / Pre-rRNA-processing protein PNO1-like / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Nin one binding (NOB1) Zn-ribbon-like / Ribosomal protein S10, eukaryotic/archaeal / RNA-binding protein NOB1 / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Ribosomal protein S11 superfamily / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribonuclease Nob1, eukaryote / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site
40S ribosomal protein S25 / 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 S24 / 40S ribosomal protein S21 / 40S ribosomal protein S28 / 40S ribosomal protein S30 ...40S ribosomal protein S25 / 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 S24 / 40S ribosomal protein S21 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / MTS domain-containing protein / 40S ribosomal protein S18 / Receptor of activated protein C kinase 1 / Pre-rRNA-processing protein TSR1 homolog / Protein LTV1 homolog / RNA-binding protein PNO1 / 40S ribosomal protein S29 / 40S ribosomal protein S15a / 40S ribosomal protein S23 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 40S ribosomal protein S9 / 40S ribosomal protein S14 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S16 / RNA-binding protein NOB1
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsAmeismeier M / Cheng J / Berninghausen O / Beckmann R
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research FoundationSFB646 Germany
German Research FoundationFOR1805 Germany
German Research FoundationGRK1721 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.
Validation ReportPDB-ID: 6g53

SummaryFull reportAbout validation report
History
DepositionMar 28, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseJun 6, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6g53
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4351.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 390.24 Å
1.08 Å/pix.
x 360 pix.
= 390.24 Å
1.08 Å/pix.
x 360 pix.
= 390.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06450907 - 0.16431251
Average (Standard dev.)0.001242415 (±0.0078486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 390.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z390.240390.240390.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0650.1640.001

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Supplemental data

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Sample components

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Entire Cryo-EM structure of a late human pre-40S ribosomal subunit - State E

EntireName: Cryo-EM structure of a late human pre-40S ribosomal subunit - State E
Number of components: 38

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Component #1: protein, Cryo-EM structure of a late human pre-40S ribosomal subu...

ProteinName: Cryo-EM structure of a late human pre-40S ribosomal subunit - State E
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA ...Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCGCCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCCUGGCGG AGCGCUGAGA AGACGGUCGA ACUUGACUAU CUAGAGGAAG UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUAA CGGAGCCCGG AG
MassTheoretical: 607.057688 kDa
SourceSpecies: Homo sapiens (human)

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Component #3: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Human (human)

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Component #4: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Human (human)

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Component #5: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Human (human)

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Component #6: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Human (human)

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Component #7: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.654869 kDa
SourceSpecies: Human (human)

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Component #8: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Human (human)

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Component #9: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Human (human)

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Component #10: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Human (human)

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Component #11: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Human (human)

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Component #12: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Human (human)

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Component #13: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Human (human)

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Component #14: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Human (human)

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Component #15: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Human (human)

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Component #16: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Human (human)

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Component #17: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Human (human)

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Component #18: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.463333 kDa
SourceSpecies: Human (human)

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Component #19: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Human (human)

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Component #20: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.668938 kDa
SourceSpecies: Human (human)

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Component #21: protein, RNA-binding protein PNO1

ProteinName: RNA-binding protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.970355 kDa
SourceSpecies: Human (human)

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Component #22: protein, RNA-binding protein NOB1

ProteinName: RNA-binding protein NOB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.743914 kDa
SourceSpecies: Human (human)

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Component #23: protein, Pre-rRNA-processing protein TSR1 homolog

ProteinName: Pre-rRNA-processing protein TSR1 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.951188 kDa
SourceSpecies: Human (human)

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Component #24: protein, Protein LTV1 homolog

ProteinName: Protein LTV1 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.935891 kDa
SourceSpecies: Human (human)

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Component #25: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.690821 kDa
SourceSpecies: Human (human)

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Component #26: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.729369 kDa
SourceSpecies: Human (human)

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Component #27: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Human (human)

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Component #28: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.933846 kDa
SourceSpecies: Human (human)

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Component #29: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Human (human)

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Component #30: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Human (human)

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Component #31: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Human (human)

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Component #32: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Human (human)

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Component #33: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Human (human)

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Component #34: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.398763 kDa
SourceSpecies: Human (human)

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Component #35: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Human (human)

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Component #36: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Human (human)

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Component #37: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Human (human)

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Component #38: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 36446
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: relion
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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Related info.:Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

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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.

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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