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- PDB-6em3: State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing th... -

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Entry
Database: PDB / ID: 6em3
TitleState A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Components
  • (5.8S ribosomal ...) x 2
  • (60S ribosomal protein ...) x 17
  • (Ribosome biogenesis protein ...) x 5
  • 25S ribosomal RNA
  • ATP-dependent RNA helicase HAS1
  • 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 / Large Subunit Biogenesis Nucleolus
Function / homology
Function and homology information


snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 ...snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / maturation of 5.8S rRNA / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / small-subunit processome / proteasome complex / macroautophagy / protein catabolic process / ribosomal small subunit biogenesis / rRNA processing / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / nuclear envelope / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / RNA helicase activity / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / cell cycle / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L36 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3450 / translation elongation factor selb, chain A, domain 4 / WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif ...Ribosomal protein L36 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3450 / translation elongation factor selb, chain A, domain 4 / WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / U3 snoRNP protein/Ribosome production factor 1 / Ubiquitin-like (UB roll) - #10 / Pescadillo / Pescadillo N-terminus / SH3 type barrels. - #30 / BRCT domain, a BRCA1 C-terminus domain / Ribosomal protein L30/S12 / Brix domain / Brix domain / Brix domain profile. / Brix / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / : / DEAD-box RNA helicase Q motif profile. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / breast cancer carboxy-terminal domain / 60S ribosomal protein L35 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L6e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L37e, conserved site / Ribosomal protein L36e signature. / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L37ae/L37e / Ribosomal Protein L6, KOW domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / 60S ribosomal protein L6E / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L37e / Ribosomal L15 / Ribosomal protein L1p/L10e family / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal proteins L26 eukaryotic, L24P archaeal
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL36B / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / rRNA-processing protein EBP2 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Proteasome-interacting protein CIC1 / Ribosome production factor 1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Large ribosomal subunit protein eL37A / Ribosome biogenesis protein NSA1 / Pescadillo homolog / Ribosome biogenesis protein 15 / Large ribosomal subunit protein eL6A / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Ribosome biogenesis protein BRX1 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKater, L. / Cheng, J. / Barrio-Garcia, C. / Hurt, E. / Beckmann, R.
CitationJournal: Cell / Year: 2017
Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
History
DepositionOct 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
x: Ribosome production factor 1
F: 60S ribosomal protein L7-A
3: Protein MAK16
4: Ribosomal RNA-processing protein 1
5: Ribosome biogenesis protein NSA1
A: Ribosome biogenesis protein BRX1
J: rRNA-processing protein EBP2
v: Nucleolar protein 16
C: 60S ribosomal protein L4-A
e: 60S ribosomal protein L32
E: 60S ribosomal protein L6-A
f: 60S ribosomal protein L33-A
G: 60S ribosomal protein L8-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-B
j: 60S ribosomal protein L37-A
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
Y: 60S ribosomal protein L26-A
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
D: ATP-dependent RNA helicase HAS1
K: Proteasome-interacting protein CIC1
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
t: Ribosome biogenesis protein RLP7
6: 5.8S ribosomal RNA
B: Ribosome biogenesis protein ERB1


Theoretical massNumber of molelcules
Total (without water)2,149,83333
Polymers2,149,83333
Non-polymers00
Water0
1


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

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Components

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Protein , 8 types, 8 molecules x34JvDKn

#1: Protein Ribosome production factor 1 / Ribosome biogenesis protein RPF1


Mass: 35184.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38805
#3: Protein Protein MAK16 / Maintenance of killer protein 16


Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10962
#4: Protein Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P35178
#7: Protein rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36049
#8: Protein Nucleolar protein 16 / Nucleolus


Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40007
#27: Protein ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q03532, RNA helicase
#28: Protein Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38779
#29: Protein Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53261

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60S ribosomal protein ... , 17 types, 17 molecules FCeEfGhijLMNOPQSY

#2: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05737
#9: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10664
#10: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38061
#11: Protein 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02326
#12: Protein 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05744
#13: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17076
#14: Protein 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX84
#15: Protein 60S ribosomal protein L36-B / Ribosome / L39 / Large ribosomal subunit protein eL36-B / YL39


Mass: 11162.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O14455
#16: Protein 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49166
#17: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12690
#18: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P36105
#19: Protein 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05748
#20: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P26784
#21: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05740
#22: Protein 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX49
#23: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX23
#24: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05743

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Ribosome biogenesis protein ... , 5 types, 5 molecules 5AotB

#5: Protein Ribosome biogenesis protein NSA1 / / NOP7-associated protein 1


Mass: 51982.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53136
#6: Protein Ribosome biogenesis protein BRX1 /


Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08235
#30: Protein Ribosome biogenesis protein 15 / / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53927
#31: Protein Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40693
#33: Protein Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q04660

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RNA chain , 1 types, 1 molecules 1

#25: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 834774822

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5.8S ribosomal ... , 2 types, 2 molecules 26

#26: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1214879358
#32: RNA chain 5.8S ribosomal RNA /


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1102641490

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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: Nsa1-TAP Flag-Ytm1 / Type: RIBOSOME
Details: Pre-60S assembly intermediates purified via Nsa1-TAP Flag-Ytm1
Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 10 / Used frames/image: 1-6

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
4GctfCTF correction
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34453 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: Backbone model

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  • 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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