EMDB-11360: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere...

Basic information

• Entry: Database: EMDB / ID: EMD-11360
• Title: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1

Sample

90S pre-ribbosome state Post-A1

• Periodic tryptophan protein 2
• (Nucleolar complex protein ...) x 2
• Something about silencing protein 10
• (U3 small nucleolar RNA-associated protein ...) x 17
• 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
• rRNA biogenesis protein RRP5
• Dimethyladenosine transferase
• Protein SOF1
• (40S ribosomal protein ...) x 17
• Pre-rRNA-processing protein PNO1
• Rps5p
• (nucleic-acidNucleic acid) x 3
• (ligand) x 3

Function / homology

Function:

18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 binding / box C/D RNA 3'-end processing / Mpp10 complex / box H/ACA snoRNA binding / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / rRNA modification / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / 90S preribosome assembly / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / box C/D RNP complex / snRNA 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 / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / 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 / 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) / enzyme activator activity / 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 / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / tRNA binding / RNA helicase / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / RNA helicase activity / cell cycle / ATPase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding

Domain/homology:

U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S13/S15, N-terminal / Helicase-associated domain / Bystin / 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 / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Sof1-like protein / Ribosomal protein L23/L15e core domain superfamily / AARP2CN / BING4, C-terminal 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 / Small-subunit processome, Utp21 / Nucleolar protein 14 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / 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 / S1 domain / HAT (Half-A-TPR) repeat / ATPase, AAA-type, core / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / NOL6/Upt22 / Small-subunit processome, Utp12 / CCAAT-binding factor / 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 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA-binding domain, S1 / 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 / 40S ribosomal protein S1/3, eukaryotes / Fibrillarin, conserved site / Ribosomal protein S17, archaeal/eukaryotic / 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 / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Nrap protein domain 1 / HEAT, type 2 / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S3Ae, conserved site / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / 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

Component:

Probable ATP-dependent RNA helicase DHR1 / rRNA-processing protein FCF1 / rRNA biogenesis protein RRP5 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 13 / 40S ribosomal protein S28-A / Ribosomal RNA small subunit methyltransferase NEP1 / 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 / U3 small nucleolar RNA-associated protein 10 / Nucleolar complex protein 14 / U3 small nucleolar RNA-associated protein MPP10 / Periodic tryptophan protein 2 / Dimethyladenosine transferase / 40S ribosomal protein S16-A / 40S ribosomal protein S5 / 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 / Ribosomal RNA-processing protein 7 / 40S ribosomal protein S7-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / Protein SOF1 / 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 / U3 small nucleolar RNA-associated protein 7 / Pre-rRNA-processing protein PNO1

• Biological species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288C (yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 3.8 Å
• Authors: Cheng J / Lau B / Venuta GL / Berninghausen O / Hurt E / Beckmann R
• Citation: Journal: 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 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 Report: Summary, Full report, XML, About validation report

History

Deposition	Jul 9, 2020	-
Header (metadata) release	Sep 23, 2020	-
Map release	Sep 23, 2020	-
Update	Sep 30, 2020	-
Current status	Sep 30, 2020	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11360.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.084 Å

Density

Contour Level	By AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum	-0.06807012 - 0.12644684
Average (Standard dev.)	0.00046802504 (±0.003439177)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 480 480 480 Spacing 480 480 480
Cell	A=B=C: 520.32 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.084	1.084	1.084
M x/y/z	480	480	480
origin x/y/z	0.000	0.000	0.000
length x/y/z	520.320	520.320	520.320
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	100	115	122
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	480	480	480
D min/max/mean	-0.068	0.126	0.000

Supplemental data

Additional map: multibody refine focus Head

• File: emd_11360_additional_1.map
• Annotation: multibody refine focus Head

Additional map: Multibody refine focus Body

• File: emd_11360_additional_2.map
• Annotation: Multibody refine focus Body

Additional map: Multibody refine focus Platform

• File: emd_11360_additional_3.map
• Annotation: Multibody refine focus Platform

Additional map: Multibody refine focus Base

• File: emd_11360_additional_4.map
• Annotation: Multibody refine focus Base

Sample components

Entire 90S pre-ribbosome state Post-A1

• Entire: Name: 90S pre-ribbosome state Post-A1 / Number of components: 67

Component #1: protein, 90S pre-ribbosome state Post-A1

• Protein: Name: 90S pre-ribbosome state Post-A1 / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

Component #2: protein, Periodic tryptophan protein 2

• Protein: Name: Periodic tryptophan protein 2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 104.097039 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #3: protein, Nucleolar complex protein 14

• Protein: Name: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 94.463195 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #4: protein, Something about silencing protein 10

• Protein: Name: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 70.364398 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 87.909242 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #6: protein, U3 small nucleolar RNA-associated protein 5

• Protein: Name: U3 small nucleolar RNA-associated protein 5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 72.079445 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #7: protein, U3 small nucleolar RNA-associated protein 6

• Protein: Name: U3 small nucleolar RNA-associated protein 6 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 52.495277 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 62.41857 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #9: protein, U3 small nucleolar RNA-associated protein 8

• Protein: Name: U3 small nucleolar RNA-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 80.269648 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 65.347254 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 200.298984 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.806348 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 12 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 106.481133 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 91.132562 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 103.18975 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #16: protein, U3 small nucleolar RNA-associated protein 15

• Protein: Name: U3 small nucleolar RNA-associated protein 15 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 57.765289 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #17: protein, Bud site selection protein 21

• Protein: Name: Bud site selection protein 21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 24.431016 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #18: protein, NET1-associated nuclear protein 1

• Protein: Name: NET1-associated nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 101.341734 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #19: protein, U3 small nucleolar RNA-associated protein 18

• Protein: Name: U3 small nucleolar RNA-associated protein 18 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 66.49425 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #20: protein, Nucleolar complex protein 4

• Protein: Name: Nucleolar complex protein 4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 63.707844 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #21: protein, U3 small nucleolar RNA-associated protein 20

• Protein: Name: U3 small nucleolar RNA-associated protein 20 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 287.9155 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #22: protein, U3 small nucleolar RNA-associated protein 21

• Protein: Name: U3 small nucleolar RNA-associated protein 21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 104.927844 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

• Protein: Name: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 140.660141 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #24: protein, rRNA-processing protein FCF1

• Protein: Name: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.650729 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #25: protein, rRNA 2'-O-methyltransferase fibrillarin

• Protein: Name: rRNA 2'-O-methyltransferase fibrillarin / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 34.525418 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #26: protein, Nucleolar protein 56

• Protein: Name: Nucleolar protein 56Nucleolus / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 56.961152 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #27: protein, Nucleolar protein 58

• Protein: Name: Nucleolar protein 58Nucleolus / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 57.060344 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #28: protein, 13 kDa ribonucleoprotein-associated protein

• Protein: Name: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 13.582855 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #29: protein, Ribosomal RNA-processing protein 9

• Protein: Name: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 65.146969 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #30: protein, U3 small nucleolar ribonucleoprotein protein IMP3

• Protein: Name: U3 small nucleolar ribonucleoprotein protein IMP3 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.928529 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #31: protein, U3 small nucleolar ribonucleoprotein protein IMP4

• Protein: Name: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 33.536168 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #32: protein, U3 small nucleolar RNA-associated protein MPP10

• Protein: Name: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 67.042492 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #33: protein, Ribosome biogenesis protein BMS1

• Protein: Name: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 135.792281 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #34: protein, RNA 3'-terminal phosphate cyclase-like protein

• Protein: Name: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 40.220559 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #35: protein, Ribosomal RNA-processing protein 7

• Protein: Name: Ribosomal RNA-processing protein 7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 34.526441 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #36: protein, Probable ATP-dependent RNA helicase DHR1

• Protein: Name: Probable ATP-dependent RNA helicase DHR1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 145.171406 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #37: protein, Ribosomal RNA small subunit methyltransferase NEP1

• Protein: Name: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 27.936461 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #38: protein, Essential nuclear protein 1

• Protein: Name: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 55.207422 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #39: protein, rRNA biogenesis protein RRP5

• Protein: Name: rRNA biogenesis protein RRP5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 193.411422 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #40: protein, Dimethyladenosine transferase

• Protein: Name: Dimethyladenosine transferase / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 36.003836 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #41: protein, rRNA-processing protein FCF2

• Protein: Name: rRNA-processing protein FCF2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 25.68924 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #42: protein, Protein SOF1

• Protein: Name: Protein SOF1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 56.888918 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #43: protein, 40S ribosomal protein S27-A

• Protein: Name: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 8.893391 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #44: protein, Pre-rRNA-processing protein PNO1

• Protein: Name: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 30.380623 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #45: protein, 40S ribosomal protein S1-A

• Protein: Name: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.798467 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #46: protein, 40S ribosomal protein S4-A

• Protein: Name: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.46933 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #47: protein, Rps5p

• Protein: Name: Rps5p / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 25.0726 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #48: protein, 40S ribosomal protein S6-A

• Protein: Name: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 27.054486 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #49: protein, 40S ribosomal protein S7-A

• Protein: Name: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 21.658209 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #50: protein, 40S ribosomal protein S8-A

• Protein: Name: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.537803 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #51: protein, 40S ribosomal protein S9-A

• Protein: Name: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.487893 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #52: protein, 40S ribosomal protein S11-A

• Protein: Name: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.785934 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #53: protein, 40S ribosomal protein S13

• Protein: Name: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.059945 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #54: protein, 40S ribosomal protein S14-A

• Protein: Name: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.562655 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #55: protein, 40S ribosomal protein S16-A

• Protein: Name: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.87749 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #56: protein, 40S ribosomal protein S18-A

• Protein: Name: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.071641 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #57: protein, 40S ribosomal protein S19-A

• Protein: Name: 40S ribosomal protein S19-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.942125 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #58: protein, 40S ribosomal protein S22-A

• Protein: Name: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.650062 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #59: protein, 40S ribosomal protein S23-A

• Protein: Name: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.073896 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #60: protein, 40S ribosomal protein S24-A

• Protein: Name: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.362848 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #61: protein, 40S ribosomal protein S28-A

• Protein: Name: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 7.605847 kDa
• Source: Species: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

Component #62: nucleic-acid, 5ETS RNA

nucleic acid

Name: 5ETS RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

UGCGAAAGCA GUUGAAGACA AGUGCUUGUC GUUCGUUAAA AUGGCCUCGU CGGAUUUGGU GGAAGGAAAC UCAAAGAGUG C

• Mass: Theoretical: 26.247596 kDa
• Source: Species: Saccharomyces cerevisiae S288C (yeast)

Component #63: nucleic-acid, 18S rRNA

nucleic acid

Name: 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 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

• Mass: Theoretical: 580.404438 kDa
• Source: Species: Saccharomyces cerevisiae S288C (yeast)

Component #64: nucleic-acid, U3 snoRNA

nucleic acid

Name: 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 CUAUAAUUUU GAAUAAAAAU UUUGCUGUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU

• Mass: Theoretical: 106.542297 kDa
• Source: Species: Saccharomyces cerevisiae S288C (yeast)

Component #65: ligand, ZINC ION

• Ligand: Name: ZINC ION / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 6.540905 MDa

Component #66: ligand, GUANOSINE-5'-TRIPHOSPHATE

• Ligand: Name: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 0.52318 kDa

Component #67: ligand, MAGNESIUM ION

• Ligand: Name: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 2.430505 MDa

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.4
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: OTHER
• Camera: Detector: FEI FALCON II (4k x 4k)

Image processing

• Processing: Method: single particle reconstruction / Number of projections: 176136
• 3D reconstruction: Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion

Atomic model buiding

Output model

6zqd