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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 / homologyP-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L22/L17 superfamily / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L7, eukaryotic/archaeal / RNA-binding domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily ...P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L22/L17 superfamily / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L7, eukaryotic/archaeal / RNA-binding domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L32e superfamily / BRCT domain superfamily / WD repeat BOP1/Erb1 / 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 L35A superfamily / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein L22p/L17e / DEAD/DEAH box helicase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L30p/L7e / Ribosomal protein L18e/L15P / Ribosomal protein L13e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L32e, 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, conserved site / Ribosome biogenesis protein BRX1 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L30, central domain, archaeal type / 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 / 60S ribosomal protein L4, C-terminal domain / Helicase conserved C-terminal domain / WD domain, G-beta repeat / Ribosomal protein L30, conserved site / Trp-Asp (WD) repeats signature. / 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 L22 signature. / Ribosomal protein L29 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30 signature. / Ribosomal protein L13 signature. / Ribosome biogenesis protein Nop16 / 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. / Domain of unknown function (DUF4217) / BOP1NT (NUC169) domain / KOW motif / Ribosomal protein L13e / 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 L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L32 / Ribosomal L30 N-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L28e protein family / Ribosomal protein L37e / Ribosomal protein L14 / Brix domain / Mak16 protein C-terminal region / Eukaryotic rRNA processing protein EBP2 / Nucleolar protein,Nop52 / Pescadillo N-terminus / Ribosomal protein L29, conserved site / WD40-repeat-containing domain / Trp-Asp (WD) repeats profile. / Ribosomal protein L15e / Ribosomal protein L29/L35 / Ribosomal protein L35A
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 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
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
Polyers2,149,83333
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 8 types, 8 molecules x34JvDKn

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


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


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


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


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


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


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


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


Mass: 69984.148 Da / Num. of mol.: 1 / 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/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05737
#9: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10664
#10: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38061
#11: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q02326
#12: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P05744
#13: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P17076
#14: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


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


Mass: 11162.285 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O14455
#16: 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 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P49166
#17: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


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


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


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


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


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


Mass: 14265.784 Da / Num. of mol.: 1 / 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/peptide Ribosome biogenesis protein NSA1 / / NOP7-associated protein 1


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


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


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


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


Mass: 91830.609 Da / Num. of mol.: 1 / 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 / 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 / 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 / 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 / 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: 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
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker'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
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
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 34453 / Symmetry type: POINT
Atomic model buildingDetails: Backbone model / Ref protocol: RIGID BODY FIT / Ref space: REAL

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