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- PDB-6cb1: Yeast nucleolar pre-60S ribosomal subunit (state 3) -

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Basic information

Entry
Database: PDB / ID: 6cb1
TitleYeast nucleolar pre-60S ribosomal subunit (state 3)
Components
  • (60S ribosomal protein ...) x 22
  • (Ribosome biogenesis protein ...) x 6
  • 35S pre-ribosomal RNA miscRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • ATP-dependent RNA helicase HAS1
  • BRX1 associated peptide
  • ITS2Internal transcribed spacer
  • Nucleolar protein 16Nucleolus
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Protein MAK16
  • Ribosomal RNA-processing protein 1
  • Ribosome production factor 1
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Pre-60S / ribosome biogenesis / LSU processome
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / snoRNA release from pre-rRNA / cell cycle DNA replication / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...L13a-mediated translational silencing of Ceruloplasmin expression / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / snoRNA release from pre-rRNA / cell cycle DNA replication / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / actomyosin contractile ring assembly / RNA-dependent ATPase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / 90S preribosome / preribosome, large subunit precursor / proteasome binding / negative regulation of mRNA splicing, via spliceosome / maturation of LSU-rRNA / ribosomal large subunit export from nucleus / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit biogenesis / proteasome complex / cytoplasmic translation / helicase activity / protein binding, bridging / protein catabolic process / large ribosomal subunit rRNA binding / rRNA processing / macroautophagy / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / nuclear envelope / ribosomal large subunit assembly / 5S rRNA binding / RNA helicase / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / RNA helicase activity / translation / cell cycle / mRNA binding / nucleolus / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Ribosomal protein L22/L17 superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L32e superfamily / BRCT domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 ...Ribosomal protein L22/L17 superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L32e superfamily / BRCT domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L14 / Ribosomal protein L7/L30 / Ribosomal protein L14, KOW motif / Ribosomal Protein L26/L24, KOW domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein L22p/L17e / RNA-binding domain superfamily / Ribosome biogenesis protein 15, RNA recognition motif / Helicase conserved C-terminal domain / Ribosomal protein L13, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosome biogenesis protein Nop16 / WD40 repeat, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 50S ribosomal protein L30e-like / Ribosomal protein L4 domain superfamily / Ribosomal protein L1-like / Ribosomal protein L15e core domain superfamily / Domain of unknown function DUF4217 / 60S ribosomal protein L4, C-terminal domain / Ribosome biogenesis protein BRX1 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / WD repeat BOP1/Erb1 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / DEAD/DEAH box helicase / Ribosomal protein L23 / Ribosomal protein L27e, conserved site / Trp-Asp (WD) repeats signature. / Domain of unknown function (DUF4217) / 60S ribosomal protein L4 C-terminal domain / BRCT domain, a BRCA1 C-terminus domain / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein 60S L18 and 50S L18e / DEAD-box subfamily ATP-dependent helicases signature. / Ribosomal protein L23 signature. / Ribosomal protein L22 signature. / Ribosomal protein L29 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30 signature. / Ribosomal protein L30e signature 1. / BOP1NT (NUC169) domain / Ribosomal protein L13 signature. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L27e signature. / Ribosomal protein L24 signature. / Ribosomal protein L34e signature. / Ribosome biogenesis protein Nop16 / Ribosomal L30 N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / WD domain, G-beta repeat / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / Ribosomal protein L1p/L10e family / Ribosomal L15 / Ribosomal L29 protein / Ribosomal protein L36e / Ribosomal protein L6e / Ribosomal protein L34e / Ribosomal protein L35Ae / Ribosomal protein L13e / Pescadillo N-terminus / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Ribosome biogenesis protein RLP7 / Protein MAK16 / 60S ribosomal protein L30 / 60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosomal RNA-processing protein 1 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Proteasome-interacting protein CIC1 / Ribosome production factor 1 ...Ribosome biogenesis protein RLP7 / Protein MAK16 / 60S ribosomal protein L30 / 60S ribosomal protein L8-A / 60S ribosomal protein L16-A / Ribosomal RNA-processing protein 1 / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / Proteasome-interacting protein CIC1 / Ribosome production factor 1 / Nucleolar protein 16 / ATP-dependent RNA helicase HAS1 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / Ribosome biogenesis protein NSA1 / Pescadillo homolog / Ribosome biogenesis protein 15 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L35-A / Ribosome biogenesis protein ERB1 / Ribosome biogenesis protein BRX1 / 60S ribosomal protein L13-A / gb:1267176496: / 60S ribosomal protein L4-A / 60S ribosomal protein L7-A / 60S ribosomal protein L18-A / Ribosomal 60S subunit protein L38 / 60S ribosomal protein L13 / Ribosomal 60S subunit protein L35A / Ribosomal 60S subunit protein L25 / Ribosomal 60S subunit protein L7A / 60S ribosomal protein L20 / RNA helicase / Ribosomal 60S subunit protein L32 / 60S ribosomal protein L6 / Ribosomal 60S subunit protein L4A / Ribosomal 60S subunit protein L18A / Ribosomal 60S subunit protein L34A / rRNA-binding ribosome biosynthesis protein / 60S ribosomal protein L20-A / Essential protein / Ribosomal 60S subunit protein L16A / Protein MAK16 / Ribosome biogenesis protein ERB1 / 60S ribosomal protein L25 / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L33-A / 60S ribosomal protein L36-A / 60S ribosomal protein L15-A / 60S ribosomal protein L27-A / gb:1104417410:
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSanghai, Z.A. / Miller, L. / Barandun, J. / Hunziker, M. / Chaker-Margot, M. / Klinge, S.
Funding support United States, Switzerland, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
National Institutes of Health/National Institute of General Medical SciencesGM115327-Tan United States
National Institutes of Health/National Institute of General Medical SciencesP41GM103314 United States
National Institutes of Health/National Institute of General Medical SciencesP41GM109824 United States
CitationJournal: Nature / Year: 2018
Title: Modular assembly of the nucleolar pre-60S ribosomal subunit.
Authors: Zahra Assur Sanghai / Linamarie Miller / Kelly R Molloy / Jonas Barandun / Mirjam Hunziker / Malik Chaker-Margot / Junjie Wang / Brian T Chait / Sebastian Klinge /
Abstract: Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly ...Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
1: 35S pre-ribosomal RNA miscRNA
2: 5.8S rRNA
6: ITS2
A: Ribosome biogenesis protein NSA1
C: 60S ribosomal protein L4-A
D: Protein MAK16
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
I: Ribosome production factor 1
K: Proteasome-interacting protein CIC1
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
S: 60S ribosomal protein L20-A
X: 60S ribosomal protein L25
Y: 60S ribosomal protein L26-A
Z: 60S ribosomal protein L27-A
7: Nucleolar protein 16
b: Ribosome biogenesis protein BRX1
c: 60S ribosomal protein L30
d: Ribosome biogenesis protein YTM1
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
k: 60S ribosomal protein L38
m: rRNA-processing protein EBP2
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
p: ATP-dependent RNA helicase HAS1
s: Ribosome biogenesis protein ERB1
t: Ribosome biogenesis protein RLP7
x: BRX1 associated peptide
z: Ribosomal RNA-processing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,185,20442
Polymers2,185,07440
Non-polymers1312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 126

#1: RNA chain 35S pre-ribosomal RNA miscRNA


Mass: 1097477.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#2: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1267176496
#3: RNA chain ITS2 / Internal transcribed spacer


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1104417410

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Ribosome biogenesis protein ... , 6 types, 6 molecules Abdost

#4: Protein/peptide Ribosome biogenesis protein NSA1 /


Mass: 51982.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53136*PLUS
#23: Protein/peptide Ribosome biogenesis protein BRX1 /


Mass: 33079.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q08235
#25: Protein/peptide Ribosome biogenesis protein YTM1 /


Mass: 39591.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#35: Protein/peptide Ribosome biogenesis protein 15 /


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53927
#37: Protein/peptide Ribosome biogenesis protein ERB1 /


Mass: 62860.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A6ZMA9, UniProt: Q04660
#38: Protein/peptide Ribosome biogenesis protein RLP7 /


Mass: 35210.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40693

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60S ribosomal protein ... , 22 types, 22 molecules CEFGLMNOPQSXYZcefghijk

#5: Protein/peptide 60S ribosomal protein L4-A / Ribosome


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WFX4, UniProt: P10664*PLUS
#7: Protein/peptide 60S ribosomal protein L6-A / Ribosome


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WFC2, UniProt: Q02326*PLUS
#8: Protein/peptide 60S ribosomal protein L7-A / Ribosome


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WCF3, UniProt: P05737*PLUS
#9: Protein/peptide 60S ribosomal protein L8-A / Ribosome


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P17076
#12: Protein/peptide 60S ribosomal protein L13-A / Ribosome


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250W9H2, UniProt: Q12690*PLUS
#13: Protein/peptide 60S ribosomal protein L14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P36105
#14: Protein/peptide 60S ribosomal protein L15-A / Ribosome


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05748
#15: Protein/peptide 60S ribosomal protein L16-A / Ribosome


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WM14, UniProt: P26784*PLUS
#16: Protein/peptide 60S ribosomal protein L17-A / Ribosome


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05740
#17: Protein/peptide 60S ribosomal protein L18-A / Ribosome


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WH37, UniProt: P0CX49*PLUS
#18: Protein/peptide 60S ribosomal protein L20-A / Ribosome


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WE58, UniProt: P0CX23*PLUS
#19: Protein/peptide 60S ribosomal protein L25 /


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WBI4, UniProt: P04456*PLUS
#20: Protein/peptide 60S ribosomal protein L26-A / Ribosome


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05743
#21: Protein/peptide 60S ribosomal protein L27-A / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P0C2H6
#24: Protein/peptide 60S ribosomal protein L30 /


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P14120
#26: Protein/peptide 60S ribosomal protein L32 /


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WF67, UniProt: P38061*PLUS
#27: Protein/peptide 60S ribosomal protein L33-A / Ribosome


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05744
#28: Protein/peptide 60S ribosomal protein L34-A / Ribosome


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WJC9, UniProt: P87262*PLUS
#29: Protein/peptide 60S ribosomal protein L35-A / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250W9S3, UniProt: P0CX84*PLUS
#30: Protein/peptide 60S ribosomal protein L36-A / Ribosome


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05745
#31: Protein/peptide 60S ribosomal protein L37-A / Ribosome


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P49166
#32: Protein/peptide 60S ribosomal protein L38 /


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WKJ9, UniProt: P49167*PLUS

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Protein/peptide , 9 types, 9 molecules DIK7mnpxz

#6: Protein/peptide Protein MAK16


Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WNS8, UniProt: P10962*PLUS
#10: Protein/peptide Ribosome production factor 1


Mass: 35184.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WKW9, UniProt: P38805*PLUS
#11: Protein/peptide Proteasome-interacting protein CIC1


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A250WL31, UniProt: P38779*PLUS
#22: Protein/peptide Nucleolar protein 16 / Nucleolus


Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40007
#33: Protein/peptide rRNA-processing protein EBP2


Mass: 8698.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#34: Protein/peptide Pescadillo homolog


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53261*PLUS
#36: Protein/peptide ATP-dependent RNA helicase HAS1


Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
References: UniProt: A0A250WER3, UniProt: Q03532*PLUS, RNA helicase
#39: Protein/peptide BRX1 associated peptide


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#40: Protein/peptide Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P35178

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Non-polymers , 1 types, 2 molecules

#41: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc

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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: Yeast nucleolar pre-60S ribosomal subunit / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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 FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.8model fitting
12RELION2.13D reconstruction
13PHENIX1.13rc1-2961model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31419 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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  • 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. See below links for details.
  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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.

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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