[English] 日本語
Yorodumi
- EMDB-4348: Cryo-EM structure of a late human pre-40S ribosomal subunit - State B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4348
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State B
Map data
SampleCryo-EM structure of a late human pre-40S ribosomal subunit - State B
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 25
  • (RNA-binding protein ...) x 2
  • Bystin
  • Pre-rRNA-processing protein TSR1 homolog
  • Protein LTV1 homolog
  • RRP12
  • Unknown
Function / homology
Function and homology information


regulation of protein localization to nucleolus / cleavage involved in rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / response to extracellular stimulus / negative regulation of RNA splicing / ubiquitin ligase inhibitor activity ...regulation of protein localization to nucleolus / cleavage involved in rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / response to extracellular stimulus / negative regulation of RNA splicing / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / activation-induced cell death of T cells / negative regulation of ubiquitin protein ligase activity / U3 snoRNA binding / erythrocyte homeostasis / translation regulator activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / erythrocyte development / TOR signaling / positive regulation of cellular component movement / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / snoRNA binding / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / T cell proliferation involved in immune response / positive regulation of ubiquitin-protein transferase activity / 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 / ribosomal small subunit export from nucleus / maturation of SSU-rRNA / regulation of translational fidelity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / translation initiation factor binding / polysome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / positive regulation of cell cycle / visual perception / erythrocyte differentiation / innate immune response in mucosa / endoribonuclease activity / polysomal ribosome / translational initiation / mRNA 3'-UTR binding / osteoblast differentiation / maintenance of translational fidelity / positive regulation of translational fidelity / presynapse / rough endoplasmic reticulum / positive regulation of translation / cytoplasmic ribonucleoprotein granule / ribosomal small subunit assembly / microtubule organizing center / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / neural tube closure / response to virus / small ribosomal subunit rRNA binding / placenta development / mRNA 5'-UTR binding / G1/S transition of mitotic cell cycle / mitotic spindle organization / rRNA processing / cytoplasmic translation / cell population proliferation / cell body / virus receptor activity / viral transcription / ribosome binding / ribosome biogenesis / glucose homeostasis / ribonucleoprotein complex / cytosolic small ribosomal subunit / small ribosomal subunit / apical part of cell / T cell differentiation in thymus / protein N-terminus binding / chromosome / killing of cells of other organism / ribosome / antibacterial humoral response / response to ethanol / protein stabilization / rRNA binding / structural constituent of ribosome / antimicrobial humoral immune response mediated by antimicrobial peptide / postsynaptic density / multicellular organism development / cadherin binding / cell differentiation / translation / cell adhesion
Ribosomal protein S17/S11 / Ribosomal protein S19/S15 / Ribosomal protein S3Ae / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / PIN domain ...Ribosomal protein S17/S11 / Ribosomal protein S19/S15 / Ribosomal protein S3Ae / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / PIN domain / Ribosomal protein S19e / RNA-binding S4 domain / K Homology domain / Ribosomal protein S25 / Ribosomal protein S5, C-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S17e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, eukaryotic / 30s ribosomal protein S13, C-terminal / Ribosomal protein S7 domain / Ribosomal protein S5/S7 / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S27 / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S19A/S15e / KOW / Bms1/Tsr1-type G domain / Ribosomal protein S3Ae, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal S24e conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S12/S23 / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S30 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Low temperature viability protein Ltv1 / Bystin / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / Ribonuclease Nob1, eukaryote / AARP2CN / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Nin one binding (NOB1) Zn-ribbon-like / Ribosomal protein S28e conserved site / Ribosomal protein S15P / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / 40S ribosomal protein SA, C-terminal domain / K Homology domain, type 1 superfamily / in:ipr038111: / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / RNA-binding protein NOB1 / Ribosomal protein S17e-like superfamily / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S21e superfamily / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosomal protein S11, N-terminal / Ribonuclease, PIN domain / Winged helix DNA-binding domain superfamily
40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / Bystin / 40S ribosomal protein S30 / 40S ribosomal protein S21 / Pre-rRNA-processing protein TSR1 homolog ...40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / Bystin / 40S ribosomal protein S30 / 40S ribosomal protein S21 / Pre-rRNA-processing protein TSR1 homolog / Protein LTV1 homolog / RNA-binding protein PNO1 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S5 / 40S ribosomal protein S18 / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S15a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 40S ribosomal protein S3a / 40S ribosomal protein S9 / 40S ribosomal protein S27 / 40S ribosomal protein S19 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S17 / RNA-binding protein NOB1
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 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 ReportSummary, Full report, XML, About validation report
History
DepositionMar 28, 2018-
Header (metadata) releaseJun 6, 2018-
Map releaseJun 6, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6g4s
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4348.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: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.0753908 - 0.203253
Average (Standard dev.)0.0013645487 (±0.009155483)
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-0.0750.2030.001

-
Supplemental data

-
Sample components

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

EntireName: Cryo-EM structure of a late human pre-40S ribosomal subunit - State B
Number of components: 34

+
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 B
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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

nucleic acidName: pre-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)

+
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)

+
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)

+
Component #5: protein, 40S ribosomal protein S27

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

+
Component #6: protein, 40S ribosomal protein S3a

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

+
Component #7: protein, 40S ribosomal protein S2

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

+
Component #8: protein, 40S ribosomal protein S28

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

+
Component #9: 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)

+
Component #10: protein, 40S ribosomal protein S30

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

+
Component #11: protein, 40S ribosomal protein S5

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

+
Component #12: protein, 40S ribosomal protein S7

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

+
Component #13: protein, 40S ribosomal protein S6

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

+
Component #14: protein, 40S ribosomal protein S25

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

+
Component #15: protein, 40S ribosomal protein S24

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

+
Component #16: protein, RNA-binding protein NOB1

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

+
Component #17: protein, RNA-binding protein PNO1

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

+
Component #18: protein, 40S ribosomal protein S23

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

+
Component #19: protein, Bystin

ProteinName: Bystin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.673258 kDa
SourceSpecies: Human (human)

+
Component #20: protein, 40S ribosomal protein S15a

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

+
Component #21: protein, 40S ribosomal protein S21

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

+
Component #22: 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)

+
Component #23: protein, Protein LTV1 homolog

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

+
Component #24: protein, 40S ribosomal protein S19

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

+
Component #25: protein, 40S ribosomal protein S18

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

+
Component #26: protein, 40S ribosomal protein S16

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

+
Component #27: protein, 40S ribosomal protein S15

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

+
Component #28: protein, 40S ribosomal protein S14

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

+
Component #29: protein, 40S ribosomal protein S13

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

+
Component #30: protein, 40S ribosomal protein S11

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

+
Component #31: protein, 40S ribosomal protein S9

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

+
Component #32: protein, 40S ribosomal protein S8

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

+
Component #33: protein, RRP12

ProteinName: RRP12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.101625 kDa
SourceSpecies: Homo sapiens (human)

+
Component #34: protein, Unknown

ProteinName: Unknown / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.79005 kDa
SourceSpecies: Homo sapiens (human)

-
Experimental details

-
Sample preparation

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

-
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)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 73661
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: relion
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

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

+
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

Read more

-
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

Read more