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- PDB-5tzs: Architecture of the yeast small subunit processome -

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Basic information

Entry
Database: PDB / ID: 5tzs
TitleArchitecture of the yeast small subunit processome
Components
  • (40S ribosomal protein ...) x 12
  • (Beta-propeller ...) x 3
  • (Kre33) x 2
  • (Nop1) x 2
  • (Repeat protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S ribosomal RNA
  • 3' domain-associated
  • 5' domain-associated
  • 5' external transcribed spacer
  • Bms1,Ribosome biogenesis protein BMS1,Bms1,Ribosome biogenesis protein BMS1
  • Enp2
  • Imp3
  • Imp4
  • Nop56
  • Nop58
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosomal RNA-processing protein 9
  • U3 small nucleolar RNA-associated protein 21,Utp21
  • U3 snoRNA
  • Unassigned KH domain
  • Unassigned RNA helices
  • Unassigned protein helices
  • Utp1
  • Utp12
  • Utp13
  • Utp17
  • Utp18
  • Utp20
  • Utp24
  • Utp30
  • Utp4
  • Utp6
  • UtpA_CTD1
  • UtpA_CTD2
  • UtpA_CTD4
KeywordsTRANSLATION / Ribosome assembly
Function / homology
Function and homology information


rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / nuclear microtubule / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / nuclear microtubule / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / rRNA base methylation / U4 snRNA binding / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U3 snoRNA binding / U4 snRNP / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / 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) / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / RNA endonuclease activity / nuclear periphery / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / ribosomal small subunit biogenesis / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase ...RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / H/ACA ribonucleoprotein complex, subunit Nhp2-like / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Quinoprotein alcohol dehydrogenase-like superfamily / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / : / Ribosomal protein S6, eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / : / Ribosomal protein L7Ae/L8/Nhp2 family / ATPase family associated with various cellular activities (AAA) / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / ATPase, AAA-type, core / 50S ribosomal protein L30e-like / : / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S9, conserved site
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS8A ...: / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsChaker-Margot, M. / Barandun, J. / Hunziker, M. / Klinge, S.
CitationJournal: Science / Year: 2017
Title: Architecture of the yeast small subunit processome.
Authors: Malik Chaker-Margot / Jonas Barandun / Mirjam Hunziker / Sebastian Klinge /
Abstract: The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of ...The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 2.0Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_entity_assembly / entity / entity_poly / entity_src_nat / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_entity_assembly.entity_id_list / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_src_nat.common_name / _entity_src_nat.pdbx_organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
0: 5' external transcribed spacer
1: 18S ribosomal RNA
2: U3 snoRNA
3: 40S ribosomal protein S6-A
5: 40S ribosomal protein S4-A
6: 40S ribosomal protein S5
7: 40S ribosomal protein S7-A
8: 40S ribosomal protein S8-A
9: 40S ribosomal protein S9-A
A: 5' domain-associated
B: 3' domain-associated
C: 40S ribosomal protein S16-A
D: 40S ribosomal protein S11-A
E: 40S ribosomal protein S22-A
F: 40S ribosomal protein S24-A
G: 40S ribosomal protein S28-A
H: Utp4
I: UtpA_CTD1
J: UtpA_CTD2
K: UtpA_CTD2
M: Beta-propeller 2
N: Utp17
O: Utp1
P: Utp6
Q: Utp12
R: Utp13
S: Utp18
T: U3 small nucleolar RNA-associated protein 21,Utp21
U: Beta-propeller 5
V: Enp2
W: UtpA_CTD4
X: Kre33
Y: Kre33
Z: Imp3
a: Nop56
b: Nop58
c: Nop1
d: Nop1
e: 13 kDa ribonucleoprotein-associated protein
f: 13 kDa ribonucleoprotein-associated protein
g: Ribosomal RNA-processing protein 9
h: RNA 3'-terminal phosphate cyclase-like protein
i: Bms1,Ribosome biogenesis protein BMS1,Bms1,Ribosome biogenesis protein BMS1
j: Ribosomal RNA small subunit methyltransferase NEP1
k: Ribosomal RNA small subunit methyltransferase NEP1
l: Utp24
m: Imp4
n: Utp30
o: Unassigned KH domain
p: Utp20
q: Repeat protein 2
r: 40S ribosomal protein S23-A
s: Beta-propeller 1
t: Beta-propeller 1
u: Beta-propeller 1
v: Repeat protein 1
y: Unassigned protein helices
z: Unassigned RNA helices


Theoretical massNumber of molelcules
Total (without water)2,258,55158
Polymers2,258,55158
Non-polymers00
Water00
1


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

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Components

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RNA chain , 3 types, 3 molecules 012

#1: RNA chain 5' external transcribed spacer


Mass: 72801.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#2: RNA chain 18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416138
#3: RNA chain U3 snoRNA


Mass: 37614.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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40S ribosomal protein ... , 12 types, 12 molecules 356789CDEFGr

#4: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX37
#5: Protein 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX35
#6: Protein 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26783
#7: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26786
#8: Protein 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX39
#9: Protein 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: O13516
#12: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX51
#13: Protein 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX47
#14: Protein 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C0W1
#15: Protein 40S ribosomal protein S24-A / RP50


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX31
#16: Protein 40S ribosomal protein S28-A / S33 / YS27


Mass: 7619.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E7X9
#49: Protein 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX29

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DNA chain , 3 types, 3 molecules ABz

#10: DNA chain 5' domain-associated


Mass: 7602.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#11: DNA chain 3' domain-associated


Mass: 21133.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#53: DNA chain Unassigned RNA helices


Mass: 14858.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Protein , 30 types, 33 molecules HIJKNOPQRSTVWXYZabcdefghijklmn...

#17: Protein Utp4


Mass: 46315.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#18: Protein UtpA_CTD1


Mass: 14996.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#19: Protein UtpA_CTD2


Mass: 9124.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#21: Protein Utp17


Mass: 46400.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#22: Protein Utp1


Mass: 54315.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#23: Protein Utp6


Mass: 26059.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#24: Protein Utp12


Mass: 60442.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#25: Protein Utp13


Mass: 61038.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#26: Protein Utp18


Mass: 21294.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#27: Protein U3 small nucleolar RNA-associated protein 21,Utp21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 83438.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae S288C (yeast), (natural) Saccharomyces cerevisiae S288c (yeast)
References: UniProt: Q06078
#29: Protein Enp2


Mass: 22400.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#30: Protein UtpA_CTD4


Mass: 8868.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#31: Protein Kre33


Mass: 54485.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#32: Protein Kre33


Mass: 54570.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#33: Protein Imp3


Mass: 12868.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#34: Protein Nop56


Mass: 26570.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#35: Protein Nop58


Mass: 29038.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#36: Protein Nop1


Mass: 18826.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#37: Protein Nop1


Mass: 18400.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#38: 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 S288C (yeast) / References: UniProt: P39990
#39: 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 S288C (yeast) / References: UniProt: Q06506
#40: 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 S288C (yeast) / References: UniProt: Q08096
#41: Protein Bms1,Ribosome biogenesis protein BMS1,Bms1,Ribosome biogenesis protein BMS1


Mass: 46598.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae S288c (yeast), (natural) Saccharomyces cerevisiae S288C (yeast)
References: UniProt: Q08965
#42: 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 S288C (yeast)
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#43: Protein Utp24


Mass: 10571.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#44: Protein Imp4


Mass: 13294.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#45: Protein Utp30


Mass: 13634.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#46: Protein Unassigned KH domain


Mass: 14911.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#47: Protein Utp20


Mass: 78654.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#52: Protein Unassigned protein helices


Mass: 43166.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Beta-propeller ... , 3 types, 5 molecules MUstu

#20: Protein Beta-propeller 2


Mass: 21974.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#28: Protein Beta-propeller 5


Mass: 24187.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#50: Protein Beta-propeller 1


Mass: 24698.311 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Repeat protein ... , 2 types, 2 molecules qv

#48: Protein Repeat protein 2


Mass: 31676.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#51: Protein Repeat protein 1


Mass: 49378.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Small subunit processome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 4 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTris(HOCH2)3CNH21
31 mMEDTA1
45 mMbiotin1
50.03 %Triton X-1001
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ted Pella Inc.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing.

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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 FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 78 K
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1714
Image scansWidth: 7420 / Height: 7676 / Movie frames/image: 32 / Used frames/image: 3-16

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2SerialEM3.5image acquisition
4CTFFIND4.0.17CTF correction
7PHENIX1.10-2155model fitting
8CootCCP4-7.0model fitting
10PHENIX1.10-2155model refinement
11RELION2initial Euler assignment
12RELION2final Euler assignment
13RELION2classification
14RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 79414
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33813 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 300 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient

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