[English] 日本語
Yorodumi
- PDB-5wyk: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-dep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wyk
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Components
  • (40S ribosomal protein ...) x 16
  • (Helical domain ...) x 2
  • (Nucleolar protein ...) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 6
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • 18S ribosomal RNA
  • 5ETS RNA
  • Enp2
  • KRR1 small subunit processome component
  • Mpp10,U3 small nucleolar RNA-associated protein MPP10
  • Periodic tryptophan protein 2
  • Pre-rRNA-processing protein PNO1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Sof1
  • U3 RNA
  • Unassigned helices
  • Utp11
  • Utp15
  • Utp17
  • Utp4
  • Utp5
  • Utp7
  • Utp8
  • Utp9
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA-processing protein FCF1
KeywordsRIBOSOME / 90S / pre-ribosome / protein-RNA complex
Function / homology
Function and homology information


regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / t-UTP complex / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation ...regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / t-UTP complex / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / septum digestion after cytokinesis / snRNA binding / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / U4/U6 snRNP / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / O-methyltransferase activity / rRNA methylation / histone H2AQ104 methyltransferase activity / Protein hydroxylation / U4 snRNP / U3 snoRNA binding / 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 / snoRNA binding / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / nucleolar large rRNA transcription by RNA polymerase I / 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 / Ub-specific processing proteases / proteasome assembly / ribosomal subunit export from nucleus / regulation of translational fidelity / 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 / ribosomal small subunit export from nucleus / RNA endonuclease activity / nuclear periphery / enzyme activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / spliceosomal complex / mRNA splicing, via spliceosome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding
Similarity search - Function
Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 ...Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / rRNA-processing protein Fcf1, PIN domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / : / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Mpp10 protein / Utp21 specific WD40 associated putative domain / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / 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 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / : / : / Eukaryotic type KH-domain (KH-domain type I) (327.11.2) / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / 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) / Anaphase-promoting complex subunit 4, WD40 domain / PIN domain / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Anaphase-promoting complex subunit 4 WD40 domain / Brix domain / Brix domain / Brix domain profile. / Brix / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Ribosome biogenesis protein UTP30 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / rRNA processing protein RCL1 / Ribosome biogenesis protein BMS1 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYe, K. / Zhu, X. / Sun, Q.
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Structure summary
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / em_software / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Data processing / Database references / Experimental summary
Data content type: EM metadata / EM metadata / EM metadata / Category: database_2 / em_admin / em_software
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6696
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3A: U3 RNA
3B: rRNA 2'-O-methyltransferase fibrillarin
3C: rRNA 2'-O-methyltransferase fibrillarin
3D: Nucleolar protein 56
3E: Nucleolar protein 58
3F: Ribosomal RNA-processing protein 9
3G: 13 kDa ribonucleoprotein-associated protein
3H: 13 kDa ribonucleoprotein-associated protein
5A: 5ETS RNA
AA: Utp4
AB: Utp5
AC: Utp8
AD: Utp9
AE: U3 small nucleolar RNA-associated protein 10
AF: Utp15
AG: Utp17
B1: Ribosome biogenesis protein BMS1
BA: Periodic tryptophan protein 2
BB: U3 small nucleolar RNA-associated protein 12
BC: U3 small nucleolar RNA-associated protein 13
BD: U3 small nucleolar RNA-associated protein 18
BE: U3 small nucleolar RNA-associated protein 21
CA: Ribosomal RNA-processing protein 7
CB: U3 small nucleolar RNA-associated protein 22
E1: Ribosomal RNA small subunit methyltransferase NEP1
E2: Ribosomal RNA small subunit methyltransferase NEP1
E4: Enp2
K1: KRR1 small subunit processome component
MA: U3 small nucleolar ribonucleoprotein protein IMP3
MB: U3 small nucleolar ribonucleoprotein protein IMP4
MC: Mpp10,U3 small nucleolar RNA-associated protein MPP10
P1: Pre-rRNA-processing protein PNO1
R1: RNA 3'-terminal phosphate cyclase-like protein
S1: Sof1
SA: 18S ribosomal RNA
SC: 40S ribosomal protein S1-A
SF: 40S ribosomal protein S4-A
SG: 40S ribosomal protein S5
SI: 40S ribosomal protein S7-A
SJ: 40S ribosomal protein S8-A
SK: 40S ribosomal protein S9-A
SM: 40S ribosomal protein S11-A
SO: 40S ribosomal protein S13
SP: 40S ribosomal protein S14-A
SR: 40S ribosomal protein S16-A
SX: 40S ribosomal protein S22-A
SY: 40S ribosomal protein S23-A
SZ: 40S ribosomal protein S24-A
Sc: 40S ribosomal protein S27-A
Sd: 40S ribosomal protein S28-A
Sf: 40S ribosomal protein S30-A
U1: Utp7
U2: Utp11
U4: rRNA-processing protein FCF1
U5: Ribosome biogenesis protein UTP30
UA: Helical domain protein
UB: Helical domain protein
UC: Unassigned helices


Theoretical massNumber of molelcules
Total (without water)3,618,02458
Polymers3,618,02458
Non-polymers00
Water00
1


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

-
Components

-
RNA chain , 3 types, 3 molecules 3A5ASA

#1: RNA chain U3 RNA


Mass: 106503.258 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
#7: RNA chain 5ETS RNA


Mass: 225543.094 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: GenBank: 1262303
#32: RNA chain 18S ribosomal RNA


Mass: 583636.562 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: GenBank: 874346701

-
Protein , 20 types, 23 molecules 3B3C3G3HAAABACADAFAGBAE1E2E4K1MCP1R1S1U1U2U4UC

#2: 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
#6: 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
#8: Protein Utp4


Mass: 66059.172 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
#9: Protein Utp5


Mass: 54740.609 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
#10: Protein Utp8


Mass: 60697.750 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
#11: Protein Utp9


Mass: 48953.438 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
#13: Protein Utp15


Mass: 43676.871 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
#14: Protein Utp17


Mass: 76271.414 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
#16: 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
#23: 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
#24: Protein Enp2


Mass: 60187.137 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
#25: 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
#28: Protein Mpp10,U3 small nucleolar RNA-associated protein MPP10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 54936.984 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: P47083
#29: 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
#30: 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
#31: Protein Sof1


Mass: 41634.328 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
#49: Protein Utp7


Mass: 47166.211 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
#50: Protein Utp11


Mass: 21294.152 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
#51: 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
#55: Protein Unassigned helices


Mass: 87930.383 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

-
Nucleolar protein ... , 2 types, 2 molecules 3D3E

#3: Protein Nucleolar protein 56 / 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
#4: Protein Nucleolar protein 58 / 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 3FCA

#5: 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
#21: 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 RNA-associated protein ... , 6 types, 6 molecules AEBBBCBDBECB

#12: 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
#17: 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
#18: 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
#19: 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 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

-
Ribosome biogenesis protein ... , 2 types, 2 molecules B1U5

#15: 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
#52: 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

-
U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules MAMB

#26: 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
#27: 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

-
40S ribosomal protein ... , 16 types, 16 molecules SCSFSGSISJSKSMSOSPSRSXSYSZScSdSf

#33: Protein 40S ribosomal protein S1-A / RP10A


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
#34: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#35: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#36: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#37: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#38: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#39: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#40: Protein 40S ribosomal protein S13 / S27a / 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
#41: Protein 40S ribosomal protein S14-A / RP59A


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
#42: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#43: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#44: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#45: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#46: Protein 40S ribosomal protein S27-A / RP61 / 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
#47: Protein 40S ribosomal protein S28-A / S33 / 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
#48: Protein 40S ribosomal protein S30-A


Mass: 7137.541 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: P0CX33

-
Helical domain ... , 2 types, 2 molecules UAUB

#53: Protein Helical domain protein


Mass: 137462.422 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
#54: Protein Helical domain protein


Mass: 84015.695 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

-
Details

Has protein modificationY
Sequence details(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they ...(1) For chains AA, AB, AC, AD, AF, AG, E4, S1, U1 and U2, The authors know the sequences, but they were unable to assign the sequences to the coordinates. The correct sequences are as follows. chain AA (UNP Q06679 1-776) MSSSLLSVLKEKSRSLKIRNKPVKMTSQERMIVHRCRFVDFTPATITSLAFSHKSNINKLTPSDLRLAIGRSNGNIEIWNPRNNWFQEMVIEGGKDRSIEGLCWSNVNGESLRLFSIGGSTVVTEWDLATGLPLRNYDCNSGVIWSISINDSQDKLSVGCDNGTVVLIDISGGPGVLEHDTILMRQEARVLTLAWKKDDFVIGGCSDGRIRIWSAQKNDENMGRLLHTMKVDKAKKESTLVWSVIYLPRTDQIASGDSTGSIKFWDFQFATLNQSFKAHDADVLCLTTDTDNNYVFSAGVDRKIFQFSQNTNKSQKNNRWVNSSNRLLHGNDIRAICAYQSKGADFLVSGGVEKTLVINSLTSFSNGNYRKMPTVEPYSKNVLVNKEQRLVVSWSESTVKIWTMGTDSSTEQNYKLVCKLTLKDDQNISTCSLSPDGQVLVVGRPSTTKVFHLQPVGNKLKVTKLDNDLLLRTSTKLVKFIDNSKIVICSCEDDVFIVDLESEEDEKPQEVELLEVTSTKSSIKVPYINRINHLEVDQNIAVISRGCGVVDILDLKARISKPLARLNNFITAVHINTSRKSVVVITADNKIYEFNMNLNSEAENEDSESVLTQWSKNNTDNLPKEWKTLKENCVGIFSDIENSSRLWFWGATWISRIDFDVDFPINKRRKQKKRTHEGLTITDESNFMNDEEDDEDDDIDMEISENLNVLLNQGNKIKSTDVQRNEESSGHFFFTDKYKPLLFVDLISSNELAIIERNPLTFHSKQKAFIQPKLVF chain AB (UNP Q04177 1-643) MDSPVLQSAYDPSGQYLCYVTVALDKQRVGVQPTQRATSSGVDTVWNENFLYLEDSKLKVTCLKWVNLASSDTVAIILGMNNGEIWLYSVLANEVTYKFTTGNSYEIKDIDLMGNQLWCIDSSDAFYQFDLLQFKLLQHFRINNCVQLNKLTIVPAGDSVAQLLVASHSISLIDIEEKKVVMTFPGHVSPVSTLQVITNEFFISGAEGDRFLNVYDIHSGMTKCVLVAESDIKELSHSGQADSIAVTTEDGSLEIFVDPLVSSSTKKRGNKSKKSSKKIQIVSKDGRKVPIYNAFINKDLLNVSWLQNATMPYFKNLQWREIPNEYTVEISLNWNNKNKSADRDLHGKDLASATNYVEGNARVTSGDNFKHVDDAIKSWERELTSLEQEQAKPPQANELLTETFGDKLESSTVARISGKKTNLKGSNLKTATTTGTVTVILSQALQSNDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLHSTLKRRSDLLPRLLALDARLDCTINKFKTLNYEAGDIHSSEPVVEEDEDDVEYNEELDDAGLIEDGEESYGSEEEEEGDSDNEEEQKHTSSKQDGRLETEQSDGEEEAGYSDVEME chain AC (UNP P53276 1-713) MPSLSQPFRLATLPKIASLSNFSLQADYVQVADGTFNESTNNITLGISGSSISQYIINPTPKLTFDYPIPSTNIITACNAEKGQANIDGNIEASTDDEANNEKTINTQKKRNVEIWAFGLMVNKGNYTLNVITKALEDTTDTSNDHLSESDIDNKAYTGSDEFLSQYKIKAKAKVMSIKIDTKNSLVIAILQNGLIEIFDFKLTLLHSFDISYDNLKYAKWFTENGTEYVFVLCPLQDDKVCYKLLELTDCGSGESSPIKELSSTIIEGFSFENSKLCYQFGKLYKLNQGKIYIYSLPHCQLQQVIEFPMVDKLSPGDDLISFQPVSVNRVLLTVNNVIYLLDLLHCSTLSQRELTHVKTFQLLKSAVINSEKSHNSKTIAIGISTKNGPNPTSSLEIINIDVGTNTLKDSLGKSFQVGNNDSSVILKPLFDDKDINDKRVKCNDVSGDSSVPVLHCNEVIEKLSALQDNDITSFDDIFFKELKIKEEHYTEKDRYISDPGFLNKVLDLIFGKFSGNDYPKTLTFLLTHPLFPLSRTRNLLSLLRDQPRLFKQAIVTCPNLPLNELLEELFSIRNRELLLDISFRILQDFTRDSIKQEMKKLSKLDVQNFIEFITSGGEDSSPECFNPSQSTQLFQLLSLVLDSIGLFSLEGALLENLTLYIDKQVEIAERNTELWNLIDTKGFQHGFASSTFDNGTSQKRALPTYTMEYLDI chain AD (UNP P38882 1-575) MGSSLDLVASFSHDSTRFAFQASVAQKNNVDIYPLNETKDYVVNSSLVSHIDYETNDMKVSDVIFFGWCSDLIDTQSSNIKRKLDEDEGTGESSEQRCENFFVNGFPDGRIVVYSSNGKDIVNIIKNKKEILGADTDESDIWILDSDKVVKKLQYNNSKPLKTFTLVDGKDDEIVHFQILHQNGTLLVCIITKQMVYIVDPSKRRPSTKYSFEISDAVACEFSSDGKYLLIANNEELIAYDLKEDSKLIQSWPVQVKTLKTLDDLIMALTTDGKINNYKIGEADKVCSIVVNEDLEIIDFTPINSKQQVLISWLNVNEPNFESISLKEIETQGYITINKNEKNNADEADQKKLEEKEEEAQPEVQHEKKETETKINKKVSKSDQVEIANILSSHLEANSTEILDDLMSGSWTEPEIKKFILTKINTVDHLSKIFLTISKSITQNPWNEENLLPLWLKWLLTLKSGELNSIKDKHTKKNCKHLKSALRSSEEILPVLLGIQGRLEMLRRQAKLREDLAQLSMQEGEDDEIEVIEHSNVISNPLQDQASPVEKLEPDSIVYANGESDEFVDASEYKD chain AF (UNP Q04305 1-513) MSTARPRIITSKAPLLPQQTTPEQRYWRQYTSAQLVKEHNSVTHISFNPQHPHDFAVTSSTRVQIFSSRTRQVIKTFSRFKDVVYSASFRSDGKLLCAGDATGLVSVYDSYNPRTILLSINASTHPTHVTKFHTQDNKILATASDDRVTRLWDISNAYEPQLELTGATDYVRTLSFIPAAPHLVATGSYDGLIRLYDTRSSGSTPIYSLNHDQPVENVIAVSPTQIVSCGGNNFKVWDLTSNKKLYERGNFNKAVTCLDYVENFDSPMQSALIASSLDGHVKVFDPLDNFQVKFGWKFSGPVLSCAVSPSTAQGNRHLVAGLSSGLLAIRTKKKEKRSSDKENAPASFNKNAKSNNFQRMMRGSEYQGDQEHIIHNDKVRSQRRMRAFERNINQFKWSEALDNAFVPGMAKELTLTVLQELRKRGKVRVALYGRDESTLEPLLNWCLKGIEDVRSASIVADWVAVVLELYGNTLESSPVLQELMIDLKTKVRHEIHKSKEAQRIEGMLQLLTS chain AG (UNP Q02931 1-896) MTQSLGIEQYKLSVVSGGKPALNNLSSVTGNKNIARLSQDQRNYIIPFNNQIKVYSVETRQCVKTLKFANNSLLSGIFLQEEENNESIVKILLGDITVPQQEDAHLITVFTNNGHVIVLNYKGKLVESPKHFKISLADEKLANVFHSEGNYRILTTFKDPSQKAHNSLQSYRLYALTFDDAKKQFEVAHQAEWHNVILSNISSNGKLLAHMCKDVSTKDHEHKSISVVSLFDDSVNLSFPLGSILSSQTQSLSYNTRYVSSMAIDNMGQQLAVGFASGVISIVSLADLQIRLLKWHIDSVLSLSFSHDGSYLLSGGWEKVMSLWQLETNSQQFLPRLNGIIIDCQVLGPQGNYYSLILQMTENNSNSDYQFLLLNASDLTSKLSINGPLPVFNSTIKHIQQPISAMNTKNSNSITSLNHSKKKQSRKLIKSRRQDFTTNVEINPINKNLYFPHISAVQIFDFYKNEQVNYQYLTSGVNNSMGKVRFELNLQDPIITDLKFTKDGQWMITYEIEYPPNDLLSSKDLTHILKFWTKNDNETNWNLKTKVINPHGISVPITKILPSPRSVNNSQGCLTADNNGGLKFWSFDSHESNWCLKKISLPNFNHFSNSVSLAWSQDGSLIFHGFDDKLQILDFDTFKKFESLENTKTVSEFTLDSEIQTVKLINDTNLIVATRTTLNAINLLRGQVINSFDLYPFVNGVYKNGHMDRLITCDERTGNIALVINQQLTDLDGVPTINYKSRIIIFDSDLSTKLGNFTHHEYISWIGWNYDTDFIFLDIESTLGVVGTTVNTQLSDEVNNEGILDGLVSNTITTSASNSDIFAEQLHKLSSRGKKSDTRDKNTNDNDEDEEDIALEFINGEKKDKLVNMNSFTSMFDNIQNVQMDTFFDRVMKVLT chain E4 (UNP P48234 1-707) MVLKSTSANDVSVYQVSGTNVSRSLPDWIAKKRKRQLKNDLEYQNRVELIQDFEFSEASNKIKVSRDGQYCMATGTYKPQIHVYDFANLSLKFDRHTDAENVDFTILSDDWTKSVHLQNDRSIQFQNKGGLHYTTRIPKFGRSLVYNKVNCDLYVGASGNELYRLNLEKGRFLNPFKLDTEGVNHVSINEVNGLLAAGTETNVVEFWDPRSRSRVSKLYLENNIDNRPFQVTTTSFRNDGLTFACGTSNGYSYIYDLRTSEPSIIKDQGYGFDIKKIIWLDNVGTENKIVTCDKRIAKIWDRLDGKAYASMEPSVDINDIEHVPGTGMFFTANESIPMHTYYIPSLGPSPRWCSFLDSITEELEEKPSDTVYSNYRFITRDDVKKLNLTHLVGSRVLRAYMHGFFINTELYDKVSLIANPDAYKDEREREIRRRIEKERESRIRSSGAVQKPKIKVNKTLVDKLSQKRGDKVAGKVLTDDRFKEMFEDEEFQVDEDDYDFKQLNPVKSIKETEEGAAKRIRALTAAEESDEERIAMKDGRGHYDYEDEESDEEESDDETNQKSNKEELSEKDLRKMEKQKALIERRKKEKEQSERFMNEMKAGTSTSTQRDESAHVTFGEQVGELLEVENGKKSNESILRRNQRGEAELTFIPQRKSKKDGNYKSRRHDNSSDEEGIDENGNKKDNGRSKPRFENRRRASKNAFRGM chain S1 (UNP P33750 1-489) MKIKTIKRSADDYVPVKSTQESQMPRNLNPELHPFERAREYTKALNATKLERMFAKPFVGQLGYGHRDGVYAIAKNYGSLNKLATGSADGVIKYWNMSTREEFVSFKAHYGLVTGLCVTQPRFHDKKPDLKSQNFMLSCSDDKTVKLWSINVDDYSNKNSSDNDSVTNEEGLIRTFDGESAFQGIDSHRENSTFATGGAKIHLWDVNRLKPVSDLSWGADNITSLKFNQNETDILASTGSDNSIVLYDLRTNSPTQKIVQTMRTNAICWNPMEAFNFVTANEDHNAYYYDMRNLSRSLNVFKDHVSAVMDVDFSPTGDEIVTGSYDKSIRIYKTNHGHSREIYHTKRMQHVFQVKYSMDSKYIISGSDDGNVRLWRSKAWERSNVKTTREKNKLEYDEKLKERFRHMPEIKRISRHRHVPQVIKKAQEIKNIELSSIKRREANERRTRKDMPYISERKKQIVGTVHKYEDSGRDRKRRKEDDKRDTQEK chain U1 (UNP P40055 1-554) MGHKKNGHRRQIKERENQNKFERSTYTNNAKNNHTQTKDKKLRAGLKKIDEQYKKAVSSAAATDYLLPESNGYLEPENELEKTFKVQQSEIKSSVDVSTANKALDLSLKEFGPYHIKYAKNGTHLLITGRKGHVASMDWRKGQLRAELFLNETCHSATYLQNEQYFAVAQKKYTFIYDHEGTELHRLKQHIEARHLDFLPYHYLLVTAGETGWLKYHDVSTGQLVSELRTKAGPTMAMAQNPWNAVMHLGHSNGTVSLWSPSMPEPLVKLLSARGPVNSIAIDRSGYYMATTGADRSMKIWDIRNFKQLHSVESLPTPGTNVSISDTGLLALSRGPHVTLWKDALKLSGDSKPCFGSMGGNPHRNTPYMSHLFAGNKVENLGFVPFEDLLGVGHQTGITNLIVPGAGEANYDALELNPFETKKQRQEQEVRTLLNKLPADTITLDPNSIGSVDKRSSTIRLNAKDLAQTTMDANNKAKTNSDIPDVKPDVKGKNSGLRSFLRKKTQNVIDERKLRVQKQLDKEKNIRKRNHQIKQGLISEDHKDVIEEALSRFG chain U2 (UNP P34247 1-250) MAKLVHDVQKKQHRERSQLTSRSRYGFLEKHKDYVKRAQDFHRKQSTLKVLREKAKERNPDEYYHAMHSRKTDAKGLLISSRHGDEEDESLSMDQVKLLKTQDSNYVRTLRQIELKKLEKGAKQLMFKSSGNHTIFVDSREKMNEFTPEKFFNTTSEMVNRSENRLTKDQLAQDISNNRNASSIMPKESLDKKKLKKFKQVKQHLQRETQLKQVQQRMDAQRELLKKGSKKKIVDSSGKISFKWKKQRKR (2) For chain MC Authors know the sequence and partially assigned the sequence (429-593) to the coordinates. The correct sequences are as follows. chain MC (UNP P47083 1-593) MSELFGVLKSNAGRIILKDPSATSKDVKAYIDSVINTCKNGSITKKAELDEITVDGLDANQVWWQVKLVLDSIDGDLIQGIQELKDVVTPSHNLSDGSTLNSSSGEESELEEAESVFKEKQMLSADVSEIEEQSNDSLSENDEEPSMDDEKTSAEAAREEFAEEKRISSGQDERHSSPDPYGINDKFFDLEKFNRDTLAAEDSNEASEGSEDEDIDYFQDMPSDDEEEEAIYYEDFFDKPTKEPVKKHSDVKDPKEDEELDEEEHDSAMDKVKLDLFADEEDEPNAEGVGEASDKNLSSFEKQQIEIRKQIEQLENEAVAEKKWSLKGEVKAKDRPEDALLTEELEFDRTAKPVPVITSEVTESLEDMIRRRIQDSNFDDLQRRTLLDITRKSQRPQFELSDVKSSKSLAEIYEDDYTRAEDESALSEELQKAHSEISELYANLVYKLDVLSSVHFVPKPASTSLEIRVETPTISMEDAQPLYMSNASSLAPQEIYNVGKAEKDGEIRLKNGVAMSKEELTREDKNRLRRALKRKRSKANLPNVNKRSKRNDVVDTLSKAKNITVINQKGEKKDVSGKTKKSRSGPDSTNIKL (3) For chains UA, UB and UC The authors don't know the sequence.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMpotassium acetateCH3COOK1
220 mMHEPES-KHEPES-K1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blot for 2 seconds before plunging

-
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: 45000 X / Calibrated magnification: 79545 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 40 e/Å2 / Film or detector model: OTHER / Num. of grids imaged: 1 / Num. of real images: 1102
Image scansWidth: 4000 / Height: 4000

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4CTF correction
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
Image processingDetails: detector is Falcon III
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 195317
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73543 / Num. of class averages: 1 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more