[English] 日本語
Yorodumi
- EMDB-6695: Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-dep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6695
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)
Map data
Sample90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
  • (nucleic-acidNucleic acid) x 3
  • rRNA 2'-O-methyltransferase fibrillarin
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • Utp4
  • Utp5
  • Utp8
  • Utp9
  • (U3 small nucleolar RNA-associated protein ...) x 6
  • Utp15
  • Utp17
  • (Ribosome biogenesis protein ...) x 2
  • Periodic tryptophan protein 2
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Essential nuclear protein 1
  • Enp2
  • KRR1 small subunit processome component
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • Mpp10,U3 small nucleolar RNA-associated protein MPP10
  • Pre-rRNA-processing protein PNO1
  • RNA 3'-terminal phosphate cyclase-like protein
  • rRNA biogenesis protein RRP5
  • Sof1
  • (40S ribosomal protein ...) x 18
  • Ubiquitin-40S ribosomal protein S31
  • Utp7
  • Utp11
  • Utp20
  • rRNA-processing protein FCF1
  • (Helical domain ...) x 2
  • Unassigned helices
Function / homology
Function and homology information


box H/ACA snoRNA binding / t-UTP complex / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snoRNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 ...box H/ACA snoRNA binding / t-UTP complex / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snoRNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / box C/D snoRNA binding / box C/D snoRNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / septum digestion after cytokinesis / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / positive regulation of RNA binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome assembly / box C/D snoRNP complex / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / single-stranded telomeric DNA binding / protein localization to nucleolus / viral genome ejection through host cell envelope, long flexible tail mechanism / U3 snoRNA binding / U4 snRNA binding / histone glutamine methylation / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / small nucleolar ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / preribosome, small subunit precursor / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 90S preribosome / O-methyltransferase activity / rRNA methylation / snoRNA binding / poly(U) RNA 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) / maturation of SSU-rRNA / regulation of translational fidelity / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / proteasome assembly / maturation of LSU-rRNA / Cajal body / endoribonuclease activity / establishment of cell polarity / positive regulation of translational fidelity / maintenance of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA 5'-UTR binding / protein tag / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / ribosome biogenesis / virion / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / protein ubiquitination / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ubiquitin protein ligase binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
S15/NS1, RNA-binding / Tetratricopeptide-like helical domain superfamily / KOW / Ribosomal protein S12/S23 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp12 / Small-subunit processome, Utp21 / Bystin ...S15/NS1, RNA-binding / Tetratricopeptide-like helical domain superfamily / KOW / Ribosomal protein S12/S23 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp12 / Small-subunit processome, Utp21 / Bystin / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S4/S9, eukaryotic/archaeal / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4e, central region / Ribosomal protein S24e / Ribosomal protein S8 / Fibrillarin / Ribosomal protein S9 / Ribosomal protein S4e / Ribosomal protein S8e / Ribosomal protein S6e / Ribosomal protein S3Ae / WD40 repeat / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / NOL6/Upt22 / Nop domain / PIN domain / Ribosomal protein S27a / RNA-binding S4 domain / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein S4e, N-terminal / Small-subunit processome, Utp13 / Bms1/Tsr1-type G domain / Periodic tryptophan protein 2 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA-binding domain, S1 / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / Phage gp6-like head-tail connector protein / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / U3 small nucleolar RNA-associated protein 10, N-terminal / HEAT, type 2 / Ribosomal protein S6, eukaryotic / Ribosomal protein S3Ae, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Fibrillarin, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat
U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S12 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / 13 kDa ribonucleoprotein-associated protein / rRNA biogenesis protein RRP5 / Ribosome biogenesis protein BMS1 ...U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / 40S ribosomal protein S12 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / 13 kDa ribonucleoprotein-associated protein / rRNA biogenesis protein RRP5 / Ribosome biogenesis protein BMS1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / Head completion protein gp15 / 40S ribosomal protein S27-A / 40S ribosomal protein S6-A / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S8-A / 40S ribosomal protein S1-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsYe K / Zhu X / Sun Q
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
Validation ReportPDB-ID: 5wyj

SummaryFull reportAbout validation report
History
DepositionJan 13, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseMar 29, 2017-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5wyj
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_6695.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 400 pix.
= 704. Å
1.76 Å/pix.
x 400 pix.
= 704. Å
1.76 Å/pix.
x 400 pix.
= 704. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.26489103 - 0.3423654
Average (Standard dev.)0.00015627964 (±0.018068692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 704.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z704.000704.000704.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2650.3420.000

-
Supplemental data

-
Sample components

+
Entire 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)

EntireName: 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
Number of components: 62

+
Component #1: protein, 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)

ProteinName: 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #2: nucleic-acid, U3 RNA

nucleic acidName: U3 RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU ...Sequence:
GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU CUAUAAUUUU GAAUAAAAAU UUUGCUUUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU
MassTheoretical: 106.503258 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #3: protein, rRNA 2'-O-methyltransferase fibrillarin

ProteinName: rRNA 2'-O-methyltransferase fibrillarin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #4: protein, Nucleolar protein 56

ProteinName: Nucleolar protein 56Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.961152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #5: protein, Nucleolar protein 58

ProteinName: Nucleolar protein 58Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.060344 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #6: protein, Ribosomal RNA-processing protein 9

ProteinName: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #7: protein, 13 kDa ribonucleoprotein-associated protein

ProteinName: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #8: nucleic-acid, 5ETS RNA

nucleic acidName: 5ETS RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU ...Sequence:
AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU GCGUAUUGAG AGAUACAAUU UGGGAAGAAA UUCCCAGAGU GUGUUUCUUU UGCGUUUAAC CUGAACAGUC UCAUCGUGGG CAUCUUGCGA UUCCAUUGGU GAGCAGCGAA GGAUUUGGUG GAUUACUAGC UAAUAGCAAU CUAUUUCAAA GAAUUCAAAC UUGGGGGAAU GCCUUGUUGA AUAGCCGGUC GCAAGACUGU GAUUCUUCAA GUGUAACCUC CUCUCAAAUC AGCGAUAUCA AACGUACCAU UCCGUGAAAC ACCGGGGUAU CUGUUUGGUG GAACCUGAUU AGAGGAAACU CAAAGAGUGC UAUGGUAUGG UGACGGAGUG CGCUGGUCAA GAGUGUAAAA GCUUUUUGAA CAGAGAGCAU UUCCGGCAGC AGAGAGACCU GAAAAAGCAA UUUUUCUGGA AUUUCAGCUG UUUCCAAACU CAAUAAGUAU CUUCUAGCAA GAGGGAAUAG GUGGGAAAAA AAAAAAGAGA UUUCGGUUUC UUUCUUUUUU ACUGCUUGUU GCUUCUUCUU UUAAGAUAGU
MassTheoretical: 225.543094 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #9: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.059172 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #10: protein, Utp5

ProteinName: Utp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.740609 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #11: protein, Utp8

ProteinName: Utp8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.69775 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #12: protein, Utp9

ProteinName: Utp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.953438 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #13: protein, U3 small nucleolar RNA-associated protein 10,Utp10

ProteinName: U3 small nucleolar RNA-associated protein 10,Utp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 173.592375 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #14: protein, Utp15

ProteinName: Utp15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.676871 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #15: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.271414 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #16: protein, Ribosome biogenesis protein BMS1

ProteinName: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.792281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #17: protein, Periodic tryptophan protein 2

ProteinName: Periodic tryptophan protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #18: protein, U3 small nucleolar RNA-associated protein 12

ProteinName: U3 small nucleolar RNA-associated protein 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.481133 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #19: protein, U3 small nucleolar RNA-associated protein 13

ProteinName: U3 small nucleolar RNA-associated protein 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.132562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #20: protein, U3 small nucleolar RNA-associated protein 18

ProteinName: U3 small nucleolar RNA-associated protein 18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #21: protein, U3 small nucleolar RNA-associated protein 21

ProteinName: U3 small nucleolar RNA-associated protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #22: protein, Ribosomal RNA-processing protein 7

ProteinName: Ribosomal RNA-processing protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #23: protein, U3 small nucleolar RNA-associated protein 22

ProteinName: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #24: protein, Ribosomal RNA small subunit methyltransferase NEP1

ProteinName: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #25: protein, Essential nuclear protein 1

ProteinName: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #26: protein, Enp2

ProteinName: Enp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.187137 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #27: protein, KRR1 small subunit processome component

ProteinName: KRR1 small subunit processome component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #28: protein, U3 small nucleolar ribonucleoprotein protein IMP3

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #29: protein, U3 small nucleolar ribonucleoprotein protein IMP4

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #30: protein, Mpp10,U3 small nucleolar RNA-associated protein MPP10

ProteinName: Mpp10,U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.936984 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #31: protein, Pre-rRNA-processing protein PNO1

ProteinName: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #32: protein, RNA 3'-terminal phosphate cyclase-like protein

ProteinName: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #33: protein, rRNA biogenesis protein RRP5

ProteinName: rRNA biogenesis protein RRP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 193.411422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #34: protein, Sof1

ProteinName: Sof1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.634328 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #35: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ...Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUUCGU GUACUGGAUU UCCAACGGGG CCUUUCCUUC UGGCUAACCU UGAGUCCUUG UGGCUCUUGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUGUUCAA AGCAGGCGUA UUGCUCGAAU AUAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUUC AAUUGUCAGA GGUGAAAUUC UUGGAUUUAU UGAAGACUAA CUACUGCGAA AGCAUUUGCC AAGGACGUUU UCAUUAAUCA AGAACGAAAG UUAGGGGAUC GAAGAUGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGACUAG GGAUCGGGUG GUGUUUUUUU AAUGACCCAC UCGGCACCUU ACGAGAAAUC AAAGUCUUUG GGUUCUGGGG GGAGUAUGGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG AGCCUGCGGC UUAAUUUGAC UCAACACGGG GAAACUCACC AGGUCCAGAC ACAAUAAGGA UUGACAGAUU GAGAGCUCUU UCUUGAUUUU GUGGGUGGUG GUGCAUGGCC GUUCUUAGUU GGUGGAGUGA UUUGUCUGCU UAAUUGCGAU AACGAACGAG ACCUUAACCU ACUAAAUAGU GGUGCUAGCA UUUGCUGGUU AUCCACUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUC UAACCUUGGC CGAGAGGUCU UGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGGAG AAUUUGGACA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA AAGAAAUUUA AU
MassTheoretical: 583.636562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #36: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.798467 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #37: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #38: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #39: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #40: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #41: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #42: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #43: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #44: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.488631 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #45: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #46: protein, 40S ribosomal protein S14-A

ProteinName: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #47: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #48: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #49: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #50: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #51: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.893391 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #52: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #53: protein, 40S ribosomal protein S30-A

ProteinName: 40S ribosomal protein S30-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.137541 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #54: protein, Ubiquitin-40S ribosomal protein S31

ProteinName: Ubiquitin-40S ribosomal protein S31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.254227 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #55: protein, Utp7

ProteinName: Utp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.166211 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #56: protein, Utp11

ProteinName: Utp11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.294152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #57: protein, Utp20

ProteinName: Utp20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 212.188828 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #58: protein, rRNA-processing protein FCF1

ProteinName: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #59: protein, Ribosome biogenesis protein UTP30

ProteinName: Ribosome biogenesis protein UTP30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #60: protein, Helical domain protein

ProteinName: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.462422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #61: protein, Helical domain protein

ProteinName: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.015695 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #62: protein, Unassigned helices

ProteinName: Unassigned helices / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.930383 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 45000.0 X (nominal), 79545.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

-
Image acquisition

Image acquisitionNumber of digital images: 2055

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 30995 / Details: detector is Falcon III
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF
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