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- PDB-6em1: State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway o... -

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Entry
Database: PDB / ID: 6em1
TitleState C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Components
  • (5.8S ribosomal ...) x 2
  • (60S ribosomal protein ...) x 20
  • (Ribosome biogenesis protein ...) x 7
  • 25S ribosomal RNA
  • ATP-dependent RNA helicase HAS1
  • Eukaryotic translation initiation factor 6
  • Nuclear GTP-binding protein NUG1
  • Nucleolar GTP-binding protein 1
  • Nucleolar protein 16Nucleolus
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Protein MAK16
  • Ribosomal RNA-processing protein 1
  • Ribosome assembly factor MRT4
  • Ribosome production factor 1
  • UPF0642 protein YBL028C
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus
Function / homologyNOG1 N-terminal helical domain / Ribosomal protein L14p/L23e / BRCT domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 / Ribosomal protein L36e domain superfamily / Ribosomal protein L7A/L8 superfamily ...NOG1 N-terminal helical domain / Ribosomal protein L14p/L23e / BRCT domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WDR74/Nsa1 / Ribosomal protein L36e domain superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L35A superfamily / Ribosomal biogenesis NSA2 family / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein L22p/L17e / DEAD/DEAH box helicase / Ribosomal protein L32e superfamily / Helicase conserved C-terminal domain / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / WD domain, G-beta repeat / Ribosomal protein L10 / 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 L22/L17 superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L24e / Nucleolar GTP-binding protein 1 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L15e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L30, central domain, archaeal type / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L1-like / Ribosomal protein L15e core domain superfamily / Domain of unknown function DUF4217 / Ribosomal L18e/L15P superfamily / 60S ribosomal protein L4, C-terminal domain / Ribosome biogenesis protein BRX1 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain / Ribosome assembly factor Mrt4 / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L7, eukaryotic/archaeal / RNA-binding domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8e / Ribosomal protein L35Ae / Ribosomal protein L3, conserved site / Eukaryotic RNA Recognition Motif (RRM) profile. / Ribosomal protein L6 signature 2. / Ribosomal protein L13 signature. / Ribosomal protein L1e signature. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L24 signature. / Ribosomal protein L6e signature. / Ribosomal protein L36e signature. / Ribosomal protein L15e signature. / Trp-Asp (WD) repeats profile. / BRCT domain profile. / Ribosomal protein L30 signature. / Trp-Asp (WD) repeats circular profile. / Brix domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / DEAD-box RNA helicase Q motif profile. / OBG-type guanine nucleotide-binding (G) domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / 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) / Insertion domain in 60S ribosomal protein L10P / Trp-Asp (WD) repeats signature. / Ribosomal protein L32e signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2017 / Release: Dec 27, 2017

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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
b: Nucleolar GTP-binding protein 1
J: rRNA-processing protein EBP2
r: Ribosome biogenesis protein NSA2
s: Nuclear GTP-binding protein NUG1
u: Ribosome biogenesis protein RLP24
v: Nucleolar protein 16
W: Ribosome assembly factor MRT4
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein YBL028C
B: 60S ribosomal protein L3
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
H: 60S ribosomal protein L9-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
V: 60S ribosomal protein L23-A
Y: 60S ribosomal protein L26-A
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
6: 5.8S ribosomal RNA
K: Proteasome-interacting protein CIC1
m: Ribosome biogenesis protein ERB1
D: ATP-dependent RNA helicase HAS1
o: Ribosome biogenesis protein 15
n: Pescadillo homolog
t: Ribosome biogenesis protein RLP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,482,06845
Polyers2,481,93743
Non-polymers1312
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)285930
ΔGint (kcal/M)-1997
Surface area (Å2)533940
MethodPISA

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Components

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Protein/peptide , 13 types, 13 molecules x34bJsvWyzKDn

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


Mass: 35184.387 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38805
#3: Protein/peptide Protein MAK16 / Maintenance of killer protein 16


Mass: 35754.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10962
#4: Protein/peptide Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35178
#7: Protein/peptide Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02892
#8: Protein/peptide rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P36049
#10: Protein/peptide Nuclear GTP-binding protein NUG1 / Nuclear GTPase 1


Mass: 57798.652 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40010
#12: Protein/peptide Nucleolar protein 16 / Nucleolus


Mass: 26954.447 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40007
#13: Protein/peptide Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33201
#14: Protein/peptide Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#15: Protein/peptide UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38202
#38: Protein/peptide Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38779
#40: Protein/peptide ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03532, RNA helicase
#42: Protein/peptide Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: YJM789 / References: UniProt: A6ZV85

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60S ribosomal protein ... , 20 types, 20 molecules FBCeEfGhHijLMNOPQSVY

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


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05737
#16: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#17: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#18: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#19: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#20: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#21: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17076
#22: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#23: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05738
#24: Protein/peptide 60S ribosomal protein L36-B / Ribosome / L39 / Large ribosomal subunit protein eL36-B / YL39


Mass: 11162.285 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O14455
#25: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#26: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#27: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36105
#28: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#29: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#30: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05740
#31: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#32: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#33: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#34: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743

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Ribosome biogenesis protein ... , 7 types, 7 molecules 5Arumot

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


Mass: 51982.457 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53136
#6: Protein/peptide Ribosome biogenesis protein BRX1 /


Mass: 33585.414 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08235
#9: Protein/peptide Ribosome biogenesis protein NSA2 / / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40078
#11: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q07915
#39: Protein/peptide Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04660
#41: Protein/peptide Ribosome biogenesis protein 15 / / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53927
#43: Protein/peptide Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40693

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

#36: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1214879358
#37: RNA chain 5.8S ribosomal RNA /


Mass: 74308.391 Da / Num. of mol.: 1 / Details: Rigid body fit based on 6ELZ
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 1102641490

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RNA chain / Non-polymers , 2 types, 3 molecules 1

#35: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: GenBank: 834774822
#44: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Nsa1-TAP Flag-Ytm1 / Type: RIBOSOME
Details: Pre-60S intermediates purified via Nsa1-TAP Flag-Ytm1
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, 41, 42, 43
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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
MicroscopyMicroscope model: 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 microns / 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
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
11RELION2.0classification
12RELION2.03D reconstruction
19REFMACmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 156937 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: Due to low local resolution, Chains 6 (ITS2), t (Rlp7), o (Nop15), n (Nop7), m (Erb1), K (Cic1) and D (Has1) of the "Foot" were rigid body docked into the EM-Map as a rigid assembly. These Chains were taken from pdb 6ELZ
Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: AVERAGE FSC

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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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