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- PDB-9n7b: SSU processome maturation and disassembly, State O -

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Basic information

Entry
Database: PDB / ID: 9n7b
TitleSSU processome maturation and disassembly, State O
Components
  • (40S ribosomal protein ...) x 18
  • (Nucleolar complex protein ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 2
  • 18S rRNA
  • Dimethyladenosine transferase
  • Essential nuclear protein 1
  • Pre-rRNA-processing protein PNO1
  • Probable ATP-dependent RNA helicase DHR1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosome biogenesis protein BMS1
  • Small ribosomal subunit protein eS1A
  • Something about silencing protein 10
  • U3 small nucleolar ribonucleoprotein protein IMP4
  • U3 snoRNA
  • U3snoRNA segment
  • rRNA-processing protein FCF1
KeywordsRIBOSOME / SSU processome / ribosome assembly / RNA folding / RNA-protein interactions
Function / homology
Function and homology information


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / RNA folding chaperone / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / ribosomal small subunit export from nucleus / RNA endonuclease activity / nuclear periphery / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / small-subunit processome / translational initiation / enzyme activator activity / helicase activity / maintenance of translational fidelity / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / RNA helicase activity / rRNA binding / structural constituent of ribosome / RNA helicase / ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleolar complex protein 4 / Nucleolar protein 14 / Nop14-like family / rRNA-processing protein Fcf1, PIN domain / Small-subunit processome, Utp14 / Utp14 protein / rRNA-processing protein Fcf1/Utp23 / Sas10 C-terminal domain / Fcf1 / Sas10 C-terminal domain ...Nucleolar complex protein 4 / Nucleolar protein 14 / Nop14-like family / rRNA-processing protein Fcf1, PIN domain / Small-subunit processome, Utp14 / Utp14 protein / rRNA-processing protein Fcf1/Utp23 / Sas10 C-terminal domain / Fcf1 / Sas10 C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / Sas10/Utp3/C1D / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / 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 / CCAAT-binding factor / CBF/Mak21 family / Bystin / Krr1, KH1 domain / Bystin / Krr1 KH1 domain / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / : / : / Eukaryotic type KH-domain (KH-domain type I) / U3 snoRNP protein/Ribosome production factor 1 / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / 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) / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / PIN domain / : / Brix domain / Brix domain / Helicase associated domain (HA2), ratchet-like / Brix domain profile. / Brix / DEAD-box helicase, OB fold / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / K Homology domain, type 1 superfamily / PIN-like domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / : / Ribosomal protein S7e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27e 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 S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal S24e conserved site
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / 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 eS19A ...GUANOSINE-5'-TRIPHOSPHATE / : / 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 eS19A / 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 uS13A / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Essential nuclear protein 1 / Dimethyladenosine transferase / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar ribonucleoprotein protein IMP4 / Probable ATP-dependent RNA helicase DHR1 / U3 small nucleolar RNA-associated protein 14 / rRNA-processing protein FCF1 / Ribosomal RNA small subunit methyltransferase NEP1 / Nucleolar complex protein 4 / rRNA processing protein RCL1 / Ribosome biogenesis protein BMS1 / Something about silencing protein 10 / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / Nucleolar complex protein 14 / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsBuzovetsky, O. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: To Be Published
Title: Mechanism of helicase-mediated SSU processome maturation and disassembly
Authors: Buzovetsky, O. / Klinge, S.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L1: 18S rRNA
L2: U3 snoRNA
L3: 40S ribosomal protein S18-A
L4: 40S ribosomal protein S4-A
L5: 40S ribosomal protein S5
L6: 40S ribosomal protein S6-A
L7: 40S ribosomal protein S7-A
L8: 40S ribosomal protein S8-A
L9: 40S ribosomal protein S9-A
LC: 40S ribosomal protein S16-A
LD: 40S ribosomal protein S11-A
LE: 40S ribosomal protein S22-A
LF: 40S ribosomal protein S24-A
LG: 40S ribosomal protein S28-A
N2: U3snoRNA segment
NA: U3 small nucleolar RNA-associated protein MPP10
NB: Something about silencing protein 10
NF: 40S ribosomal protein S13
NG: 40S ribosomal protein S14-A
NL: Dimethyladenosine transferase
NM: Small ribosomal subunit protein eS1A
NP: 40S ribosomal protein S19-A
NQ: 40S ribosomal protein S27-A
NS: Probable ATP-dependent RNA helicase DHR1
NW: 40S ribosomal protein S25-A
SH: RNA 3'-terminal phosphate cyclase-like protein
SI: Ribosome biogenesis protein BMS1
SJ: Ribosomal RNA small subunit methyltransferase NEP1
SK: Ribosomal RNA small subunit methyltransferase NEP1
SL: rRNA-processing protein FCF1
SM: U3 small nucleolar ribonucleoprotein protein IMP4
SR: 40S ribosomal protein S23-A
SS: U3 small nucleolar RNA-associated protein 14
ST: Nucleolar complex protein 14
SU: Nucleolar complex protein 4
SW: Pre-rRNA-processing protein PNO1
SZ: Essential nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,993,70787
Polymers1,991,91137
Non-polymers1,79650
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L1L2N2

#1: RNA chain 18S rRNA


Mass: 580765.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: GenBank: 1262303
#2: RNA chain U3 snoRNA


Mass: 106943.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
#15: RNA chain U3snoRNA segment


Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741

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40S ribosomal protein ... , 18 types, 18 molecules L3L4L5L6L7L8L9LCLDLELFLGNFNGNPNQNWSR

#3: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P0CX55
#4: 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) / Cell line: BY4741 / References: UniProt: P0CX35
#5: 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) / Cell line: BY4741 / References: UniProt: P26783
#6: 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) / Cell line: BY4741 / References: UniProt: P0CX37
#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) / Cell line: BY4741 / 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) / Cell line: BY4741 / 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) / Cell line: BY4741 / References: UniProt: O13516
#10: 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) / Cell line: BY4741 / References: UniProt: P0CX51
#11: 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) / Cell line: BY4741 / References: UniProt: P0CX47
#12: 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) / Cell line: BY4741 / References: UniProt: P0C0W1
#13: 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) / Cell line: BY4741 / References: UniProt: P0CX31
#14: Protein 40S ribosomal protein S28-A / 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q3E7X9
#18: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P05756
#19: Protein 40S ribosomal protein S14-A / 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P06367
#22: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P07280
#23: Protein 40S ribosomal protein S27-A / 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P35997
#25: Protein 40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q3E792
#31: 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) / Cell line: BY4741 / References: UniProt: P0CX29

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U3 small nucleolar RNA-associated protein ... , 2 types, 2 molecules NASS

#16: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P47083
#32: Protein U3 small nucleolar RNA-associated protein 14 / U3 snoRNA-associated protein 14 / U three protein 14


Mass: 103269.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04500

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Protein , 11 types, 12 molecules NBNLNMNSSHSISJSKSLSMSWSZ

#17: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q12136
#20: Protein Dimethyladenosine transferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S- ...18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / 18S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 36003.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741
References: UniProt: P41819, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#21: Protein Small ribosomal subunit protein eS1A / 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P33442
#24: Protein Probable ATP-dependent RNA helicase DHR1 / DEAH box RNA helicase DHR1 / Extracellular mutant protein 16


Mass: 145171.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q04217, RNA helicase
#26: 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) / Cell line: BY4741 / References: UniProt: Q08096
#27: Protein Ribosome biogenesis protein BMS1


Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: Q08965
#28: 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) / Cell line: BY4741
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#29: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q05498
#30: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: P53941
#35: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q99216
#36: Protein Essential nuclear protein 1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Cell line: BY4741 / References: UniProt: P38333

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

#33: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q99207
#34: 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 S288C (yeast) / Cell line: BY4741 / References: UniProt: Q06512

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Non-polymers , 3 types, 50 molecules

#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION


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


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

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Details

Has ligand of interestN
Has protein modificationY

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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: SSU processome maturation and disassembly, State O / Type: COMPLEX / Entity ID: #1-#36 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
160 mMTris-HCl1
250 mMNaCl1
35 mMMgCl1
42 %glycerol1
50.01 %NP-401
61 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 61.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131106 / Symmetry type: POINT

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

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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

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