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- PDB-6zqb: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

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Entry
Database: PDB / ID: 6zqb
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2
Components
  • (40S ribosomal protein ...) x 16
  • (Nucleolar complex protein ...) x 2
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • (U3 small nucleolar RNA-associated protein ...) x 17
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • (rRNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S rRNA18S ribosomal RNA
  • 5ETS RNA
  • Bud site selection protein 21
  • Essential nuclear protein 1
  • KRR1 small subunit processome component
  • NET1-associated nuclear protein 1
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • Protein BFR2
  • Protein FAF1
  • Protein SOF1
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • Regulator of rDNA transcription protein 14
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Rps5p
  • Something about silencing protein 10
  • U3 snoRNA
  • rRNA 2'-O-methyltransferase fibrillarin
KeywordsRIBOSOME / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1
Function / homology
Function and homology information


rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / tRNA acetylation / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process ...rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / tRNA acetylation / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / mRNA modification / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase 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 / nuclear microtubule / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / small nuclear ribonucleoprotein complex / 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 / 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 / nuclear periphery / proteasome assembly / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / vesicle-mediated transport / 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) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / protein transport / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / 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 L1p/L10e family / Helix hairpin bin domain superfamily / Regulator of rDNA transcription 14 / Bms1/Tsr1-type G domain / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S28e conserved site ...Ribosomal protein L1p/L10e family / Helix hairpin bin domain superfamily / Regulator of rDNA transcription 14 / Bms1/Tsr1-type G domain / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S28e conserved site / 40S ribosomal protein S11, N-terminal / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / Possible tRNA binding domain / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleolar complex protein 4 / Periodic tryptophan protein 2 / 40S ribosomal protein S4, C-terminal domain / TmcA/NAT10/Kre33 / Anaphase-promoting complex subunit 4, WD40 domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / WD40-repeat-containing domain superfamily / RNA cytidine acetyltransferase NAT10 / Nop domain superfamily / Ribosomal protein S8 superfamily / Nrap protein, domain 6 / Nrap protein, domain 5 / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Nrap protein domain 1 / AATF leucine zipper-containing domain / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase type 2 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Armadillo-type fold / Ribosomal protein S8e, conserved site / WD40/YVTN repeat-like-containing domain superfamily / Fcf2 pre-rRNA processing, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp13 / Ribosomal protein S4e, central region / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal RNA assembly KRR1 / HEAT, type 2 / Ribosomal protein S7 domain / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein L1-like / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10, N-terminal / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 8 / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / WD40 repeat, conserved site / U3 small nucleolar RNA-associated protein 15, C-terminal / Sas10 C-terminal domain / Protein AATF/Bfr2 / Ribosome biogenesis protein Bms1/Tsr1 / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Bystin / Dip2/Utp12 Family / Regular of rDNA transcription protein 14 / Sof1-like domain / Fcf2 pre-rRNA processing / Apoptosis antagonizing transcription factor / Apoptosis-antagonizing transcription factor, C-terminal / Krr1 KH1 domain / EMG1/NEP1 methyltransferase / Sas10 C-terminal domain / Sas10/Utp3/C1D family / NUC153 domain / Possible tRNA binding domain / GNAT acetyltransferase 2 / Domain of unknown function (DUF1726)
40S ribosomal protein S16-A / Periodic tryptophan protein 2 / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S7-A / 40S ribosomal protein S5 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / Ribosomal RNA-processing protein 7 ...40S ribosomal protein S16-A / Periodic tryptophan protein 2 / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S7-A / 40S ribosomal protein S5 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / 40S ribosomal protein S11-A / 40S ribosomal protein S23-A / 40S ribosomal protein S24-A / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S4-A / 40S ribosomal protein S6-A / 40S ribosomal protein S8-A / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S18-A / 40S ribosomal protein S1-A / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 20 / Nucleolar protein 56 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Pre-rRNA-processing protein PNO1 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / Nucleolar protein 58 / U3 small nucleolar RNA-associated protein 12 / U3 small nucleolar RNA-associated protein 15 / Something about silencing protein 10 / rRNA-processing protein FCF2 / Ribosome biogenesis protein BMS1 / Bud site selection protein 21 / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 4 / Protein BFR2 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 5 / 40S ribosomal protein S27-A / Regulator of rDNA transcription protein 14 / Ribosomal RNA-processing protein 9 / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / Protein FAF1 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / RNA cytidine acetyltransferase / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / Protein SOF1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCheng, J. / Lau, B. / Venuta, G.L. / 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 Report
SummaryFull reportAbout validation report
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
UA: Periodic tryptophan protein 2
UB: Nucleolar complex protein 14
UC: Something about silencing protein 10
UD: U3 small nucleolar RNA-associated protein 4
UE: U3 small nucleolar RNA-associated protein 5
UF: U3 small nucleolar RNA-associated protein 6
UG: U3 small nucleolar RNA-associated protein 7
UH: U3 small nucleolar RNA-associated protein 8
UI: U3 small nucleolar RNA-associated protein 9
UJ: U3 small nucleolar RNA-associated protein 10
UK: U3 small nucleolar RNA-associated protein 11
UL: U3 small nucleolar RNA-associated protein 12
UM: U3 small nucleolar RNA-associated protein 13
UN: U3 small nucleolar RNA-associated protein 14,U3 small nucleolar RNA-associated protein 14
UO: U3 small nucleolar RNA-associated protein 15
UP: Bud site selection protein 21
UQ: NET1-associated nuclear protein 1
UR: U3 small nucleolar RNA-associated protein 18
US: Nucleolar complex protein 4
UT: U3 small nucleolar RNA-associated protein 20
UU: U3 small nucleolar RNA-associated protein 21
UV: U3 small nucleolar RNA-associated protein 22
UX: rRNA-processing protein FCF1
UZ: Ribosome biogenesis protein UTP30
CA: rRNA 2'-O-methyltransferase fibrillarin
CB: rRNA 2'-O-methyltransferase fibrillarin
CD: Nucleolar protein 56
CE: Nucleolar protein 58
CF: 13 kDa ribonucleoprotein-associated protein
CG: 13 kDa ribonucleoprotein-associated protein
CH: Ribosomal RNA-processing protein 9
CI: U3 small nucleolar ribonucleoprotein protein IMP3
CJ: U3 small nucleolar ribonucleoprotein protein IMP4
CK: U3 small nucleolar RNA-associated protein MPP10
CL: Ribosome biogenesis protein BMS1
CM: RNA 3'-terminal phosphate cyclase-like protein
CN: Ribosomal RNA-processing protein 7
JA: RNA cytidine acetyltransferase
JB: RNA cytidine acetyltransferase
JC: Ribosome biogenesis protein ENP2
JE: U3 small nucleolar ribonucleoprotein protein LCP5
JF: Ribosomal RNA small subunit methyltransferase NEP1
JG: Ribosomal RNA small subunit methyltransferase NEP1
JH: Essential nuclear protein 1
JJ: Pre-rRNA-processing protein PNO1
JK: Protein BFR2
JM: rRNA-processing protein FCF2
JN: Protein FAF1
JO: KRR1 small subunit processome component
JP: Protein SOF1
JQ: Regulator of rDNA transcription protein 14
DA: 40S ribosomal protein S1-A
DE: 40S ribosomal protein S4-A
DF: Rps5p
DG: 40S ribosomal protein S6-A
DH: 40S ribosomal protein S7-A
DI: 40S ribosomal protein S8-A
DJ: 40S ribosomal protein S9-A
DL: 40S ribosomal protein S11-A
DN: 40S ribosomal protein S13
DO: 40S ribosomal protein S14-A
DQ: 40S ribosomal protein S16-A
DS: 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18
DW: 40S ribosomal protein S22-A
DX: 40S ribosomal protein S23-A
DY: 40S ribosomal protein S24-A
Db: 40S ribosomal protein S27-A
Dc: 40S ribosomal protein S28-A
D2: 5ETS RNA
D3: 18S rRNA
D4: U3 snoRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,576,42874
Polymers4,575,77471
Non-polymers6543
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 17 types, 21 molecules UAUCUPUQCACBCFCGCMJAJBJFJGJHJJJKJNJOJPJQDF

#1: Protein Periodic tryptophan protein 2 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25635
#3: Protein Something about silencing protein 10 / U three protein 3 / U3 small nucleolar RNA-associated protein 3 / U3 snoRNA-associated protein 11


Mass: 70364.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12136
#16: Protein Bud site selection protein 21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16


Mass: 24431.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08492
#17: Protein NET1-associated nuclear protein 1 / U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA- ...U three protein 17 / t-17 / U3 protein 17 required for transcription / U3 small nucleolar RNA-associated protein 17 / U3 snoRNA-associated protein 17


Mass: 101341.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02931
#25: Protein rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1


Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#28: Protein 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39990
#34: Protein RNA 3'-terminal phosphate cyclase-like protein


Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08096
#36: Protein RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine ...18S rRNA cytosine acetyltransferase / Killer toxin-resistance protein 33 / Ribosomal RNA cytidine acetyltransferase 1


Mass: 119509.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#39: Protein Ribosomal RNA small subunit methyltransferase NEP1 / / 18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / ...18S rRNA (pseudouridine(1189)-N1)-methyltransferase / 18S rRNA Psi1189 methyltransferase / Essential for mitotic growth protein 1 / Nucleolar essential protein 1


Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#40: Protein Essential nuclear protein 1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38333
#41: Protein Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99216
#42: Protein Protein BFR2 / Brefeldin A resistance protein 2


Mass: 61285.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06631
#44: Protein Protein FAF1 / Forty S assembly factor


Mass: 38961.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40546
#45: Protein KRR1 small subunit processome component / / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1


Mass: 37226.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25586
#46: Protein Protein SOF1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1


Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33750
#47: Protein Regulator of rDNA transcription protein 14


Mass: 23898.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40470
#50: Protein Rps5p


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783

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Nucleolar complex protein ... , 2 types, 2 molecules UBUS

#2: Protein Nucleolar complex protein 14 / U three protein 2 / U3 small nucleolar RNA-associated protein 2 / U3 snoRNA-associated protein 2


Mass: 94463.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99207
#19: Protein Nucleolar complex protein 4 / U three protein 19 / U3 small nucleolar RNA-associated protein 19 / U3 snoRNA-associated protein 19


Mass: 63707.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06512

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U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules UDUEUFUGUHUIUJUKULUMUNUOURUTUUUVCK

#4: Protein U3 small nucleolar RNA-associated protein 4 / U3 snoRNA-associated protein 4 / U three protein 4 / U3 protein 4 required for transcription / t-UTP4


Mass: 87909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06679
#5: Protein U3 small nucleolar RNA-associated protein 5 / U3 snoRNA-associated protein 5 / U three protein 5 / U3 protein 5 required for transcription / t-UTP5


Mass: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04177
#6: Protein U3 small nucleolar RNA-associated protein 6 / U3 snoRNA-associated protein 6 / U three protein 6


Mass: 52495.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02354
#7: Protein U3 small nucleolar RNA-associated protein 7 / U3 snoRNA-associated protein 7 / U three protein 7


Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40055
#8: Protein U3 small nucleolar RNA-associated protein 8 / U3 snoRNA-associated protein 8 / U three protein 8 / U3 protein 8 required for transcription / t-UTP8


Mass: 80269.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53276
#9: Protein U3 small nucleolar RNA-associated protein 9 / U3 snoRNA-associated protein 9 / U three protein 9 / U3 protein 9 required for transcription / t-UTP9


Mass: 65347.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38882
#10: Protein U3 small nucleolar RNA-associated protein 10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10


Mass: 200298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P42945
#11: Protein U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / U three protein 11


Mass: 29806.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P34247
#12: Protein U3 small nucleolar RNA-associated protein 12 / U3 snoRNA-associated protein 12 / DOM34-interacting protein 2 / U three protein 12


Mass: 106481.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12220
#13: Protein U3 small nucleolar RNA-associated protein 13 / U3 snoRNA-associated protein 13 / U three protein 13


Mass: 91132.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05946
#14: Protein U3 small nucleolar RNA-associated protein 14,U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14


Mass: 17147.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04500
#15: Protein U3 small nucleolar RNA-associated protein 15 / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for transcription / t-UTP15


Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04305
#18: Protein U3 small nucleolar RNA-associated protein 18 / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40362
#20: Protein U3 small nucleolar RNA-associated protein 20 / U3 snoRNA-associated protein 20 / U three protein 20


Mass: 287915.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35194
#21: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06078
#22: Protein U3 small nucleolar RNA-associated protein 22 / U3 snoRNA-associated protein 22 / U three protein 22


Mass: 140660.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53254
#32: Protein U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47083

+
RRNA-processing protein ... , 2 types, 2 molecules UXJM

#23: Protein rRNA-processing protein FCF1 / FAF1-copurifying factor 1


Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05498
#43: Protein rRNA-processing protein FCF2 / FAF1 copurifying factor 2


Mass: 25689.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12035

+
Ribosome biogenesis protein ... , 3 types, 3 molecules UZCLJC

#24: Protein Ribosome biogenesis protein UTP30 / / U3 snoRNP-associated protein UTP30


Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36144
#33: Protein Ribosome biogenesis protein BMS1 /


Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08965
#37: Protein Ribosome biogenesis protein ENP2 / / Essential nuclear protein 2


Mass: 81864.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48234

+
Nucleolar protein ... , 2 types, 2 molecules CDCE

#26: Protein Nucleolar protein 56 / Nucleolus / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1


Mass: 56961.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12460
#27: Protein Nucleolar protein 58 / Nucleolus / Nucleolar protein 5


Mass: 57060.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12499

+
Ribosomal RNA-processing protein ... , 2 types, 2 molecules CHCN

#29: Protein Ribosomal RNA-processing protein 9


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06506
#35: Protein Ribosomal RNA-processing protein 7


Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25368

+
U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules CICJJE

#30: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32899
#31: Protein U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Interacting with MPP10 protein 4


Mass: 33536.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53941
#38: Protein U3 small nucleolar ribonucleoprotein protein LCP5


Mass: 40864.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40079

+
40S ribosomal protein ... , 16 types, 16 molecules DADEDGDHDIDJDLDNDODQDSDWDXDYDbDc

#48: Protein 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#49: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#51: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#52: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#53: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#54: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#55: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#56: Protein 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#57: Protein 40S ribosomal protein S14-A / Ribosome / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06367
#58: Protein 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#59: Protein 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18 / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 16303.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288C (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#60: Protein 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#61: Protein 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#62: Protein 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#63: Protein 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#64: Protein 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9

+
RNA chain , 3 types, 3 molecules D2D3D4

#65: RNA chain 5ETS RNA


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#66: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 582381.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#67: RNA chain U3 snoRNA


Mass: 56132.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

+
Non-polymers , 2 types, 3 molecules

#68: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#69: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 90S pre-ribosome state B2 / Type: RIBOSOME / Entity ID: #1-#67 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32213 / Symmetry type: POINT

+
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