[English] 日本語
Yorodumi
- EMDB-11361: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11361
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala)
Map data
Sample90S pre-ribbosome state Dis-A
  • Periodic tryptophan protein 2
  • (Nucleolar complex protein ...) x 2
  • Something about silencing protein 10
  • (U3 small nucleolar RNA-associated protein ...) x 15
  • Bud site selection protein 21
  • NET1-associated nuclear protein 1
  • (rRNA-processing protein ...) x 2
  • rRNA 2'-O-methyltransferase fibrillarin
  • (Nucleolar protein ...Nucleolus) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • (Ribosomal RNA-processing protein ...) x 2
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • Ribosome biogenesis protein BMS1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Probable ATP-dependent RNA helicase DHR1
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Essential nuclear protein 1
  • Dimethyladenosine transferase
  • (40S ribosomal protein ...) x 18
  • Pre-rRNA-processing protein PNO1
  • (nucleic-acidNucleic acid) x 3
  • ligand
Function / homology
Function and homology information


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / rDNA heterochromatin / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / snRNA binding / rRNA primary transcript binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / sno(s)RNA-containing ribonucleoprotein complex / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA 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 / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / RNA helicase / structural constituent of ribosome / mitochondrial matrix / cell cycle / translation / RNA helicase activity / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Ribosomal RNA adenine dimethylase / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 ...Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc-binding ribosomal protein / Down-regulated-in-metastasis protein / Ribosomal RNA adenine dimethylase / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / AARP2CN / Helicase-associated domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / U3 snoRNA associated / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Small-subunit processome, Utp13 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S6, eukaryotic / Bystin / Small-subunit processome, Utp21 / Ribosomal protein L2, domain 2 / NOL6/Upt22 / Ribosomal protein S11 / Ribosomal protein S24e / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Nop domain / PIN domain / RNA-binding S4 domain / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / CCAAT-binding factor / Nucleolar protein 14 / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / KOW / Ribosomal protein S12/S23 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Ribosomal protein S5 domain 2-type fold, subgroup / Fcf2 pre-rRNA processing, C-terminal / Ribosomal protein S13 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S4/S9 / Ribosomal protein S15P / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S28e conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / 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 / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / Nrap protein, domain 2 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / HEAT, type 2 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S8e, conserved site / 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 S13, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Fibrillarin, conserved site
U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / Ribosomal RNA small subunit methyltransferase NEP1 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 8 ...U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / Ribosomal RNA small subunit methyltransferase NEP1 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 22 / NET1-associated nuclear protein 1 / Nucleolar complex protein 14 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / Ribosomal RNA-processing protein 7 / Dimethyladenosine transferase / 40S ribosomal protein S16-A / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S19-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / 40S ribosomal protein S11-A / 40S ribosomal protein S18-A / U3 small nucleolar RNA-associated protein 18 / rRNA 2'-O-methyltransferase fibrillarin / Periodic tryptophan protein 2 / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / U3 small nucleolar RNA-associated protein 11 / U3 small nucleolar RNA-associated protein 20 / 40S ribosomal protein S27-A / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsCheng J / Lau B / Venuta GL / Berninghausen O / Hurt E / Beckmann R
CitationJournal: Science / Year: 2020
Title: 90 pre-ribosome transformation into the primordial 40 subunit.
Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 9, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zqe
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_11361.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.32 Å
1.06 Å/pix.
x 480 pix.
= 508.32 Å
1.06 Å/pix.
x 480 pix.
= 508.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.012674955 - 0.036449794
Average (Standard dev.)0.00027297647 (±0.0016071454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.320508.320508.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0130.0360.000

-
Supplemental data

-
Sample components

+
Entire 90S pre-ribbosome state Dis-A

EntireName: 90S pre-ribbosome state Dis-A / Number of components: 61

+
Component #1: protein, 90S pre-ribbosome state Dis-A

ProteinName: 90S pre-ribbosome state Dis-A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #2: 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 #3: protein, Nucleolar complex protein 14

ProteinName: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.463195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #4: protein, Something about silencing protein 10

ProteinName: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.364398 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #5: protein, U3 small nucleolar RNA-associated protein 4

ProteinName: U3 small nucleolar RNA-associated protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.909242 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #6: protein, U3 small nucleolar RNA-associated protein 9

ProteinName: U3 small nucleolar RNA-associated protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.347254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #7: protein, U3 small nucleolar RNA-associated protein 8

ProteinName: U3 small nucleolar RNA-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.269648 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #8: protein, U3 small nucleolar RNA-associated protein 5

ProteinName: U3 small nucleolar RNA-associated protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #9: protein, U3 small nucleolar RNA-associated protein 10

ProteinName: U3 small nucleolar RNA-associated protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 200.298984 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #10: protein, U3 small nucleolar RNA-associated protein 11

ProteinName: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #11: 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 #12: 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 #13: protein, U3 small nucleolar RNA-associated protein 14

ProteinName: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.518649 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #14: protein, U3 small nucleolar RNA-associated protein 15

ProteinName: U3 small nucleolar RNA-associated protein 15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #15: protein, Bud site selection protein 21

ProteinName: Bud site selection protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.431016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #16: protein, NET1-associated nuclear protein 1

ProteinName: NET1-associated nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.341734 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #17: 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 #18: protein, Nucleolar complex protein 4

ProteinName: Nucleolar complex protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.707844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #19: protein, U3 small nucleolar RNA-associated protein 20

ProteinName: U3 small nucleolar RNA-associated protein 20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 287.9155 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #20: 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 #21: 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 #22: 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 #23: 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 #24: 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 #25: 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 #26: 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 #27: 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 #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, U3 small nucleolar RNA-associated protein MPP10

ProteinName: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #31: 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 #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, 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 #34: protein, Probable ATP-dependent RNA helicase DHR1

ProteinName: Probable ATP-dependent RNA helicase DHR1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 145.171406 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #35: 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 #36: 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 #37: protein, Dimethyladenosine transferase

ProteinName: Dimethyladenosine transferase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.003836 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #38: protein, rRNA-processing protein FCF2

ProteinName: rRNA-processing protein FCF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #39: 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 #40: 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 #41: 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 #42: 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 #43: 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 #44: 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 #45: 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 #46: 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 #47: 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 #48: 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 #49: 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 #50: 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 #51: 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 #52: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.071641 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #53: protein, 40S ribosomal protein S19-A

ProteinName: 40S ribosomal protein S19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.942125 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #54: 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 #55: 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 #56: 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 #57: 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 #58: nucleic-acid, 5ETS RNA

nucleic acidName: 5ETS RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCGAAAGCA GUUGAAGACA AGUGCUUGUC GUUCGUUAAA AUGGCCUCGU CGGAUUUGGU GGAAGGAAAC UCAAAGAGUG C
MassTheoretical: 26.247596 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #59: nucleic-acid, 18S rRNA

nucleic acidName: 18S rRNA18S 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 CGCAAGGCUA 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 AA
MassTheoretical: 580.404438 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #60: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / 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 UUUGCUGUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU
MassTheoretical: 106.542297 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #61: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
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: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 11312
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
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