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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
DescriptorRibosome production factor 1
Protein MAK16
Ribosomal RNA-processing protein 1
rRNA-processing protein EBP2
Nucleolar protein 16
and more 5 items
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsKater, L. / Cheng, J. / Barrio-Garcia, C. / Hurt, E. / Beckmann, R.
CitationCell, 2017, 171, 1599-1610.e14

Cell, 2017, 171, 1599-1610.e14 Yorodumi Papers
Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
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

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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Polypeptide(L) , 8 types, 8 molecules x34JvDKn

#1: Polypeptide(L)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)
References: UniProt: P38805
#3: Polypeptide(L)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)
References: UniProt: P10962
#4: Polypeptide(L)Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P35178
#7: Polypeptide(L)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)
References: UniProt: P36049
#8: Polypeptide(L)Nucleolar protein 16


Mass: 26954.447 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40007
#27: Polypeptide(L)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)
References: UniProt: Q03532, EC: 3.6.4.13
#28: Polypeptide(L)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)
References: UniProt: P38779
#29: Polypeptide(L)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)
References: UniProt: P53261

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

#2: Polypeptide(L)60S ribosomal protein L7-A / 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)
References: UniProt: P05737
#9: Polypeptide(L)60S ribosomal protein L4-A / 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)
References: UniProt: P10664
#10: Polypeptide(L)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)
References: UniProt: P38061
#11: Polypeptide(L)60S ribosomal protein L6-A / 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)
References: UniProt: Q02326
#12: Polypeptide(L)60S ribosomal protein L33-A / 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)
References: UniProt: P05744
#13: Polypeptide(L)60S ribosomal protein L8-A / 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)
References: UniProt: P17076
#14: Polypeptide(L)60S ribosomal protein L35-A / 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)
References: UniProt: P0CX84
#15: Polypeptide(L)60S ribosomal protein L36-B / 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)
References: UniProt: O14455
#16: Polypeptide(L)60S ribosomal protein L37-A / 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)
References: UniProt: P49166
#17: Polypeptide(L)60S ribosomal protein L13-A / 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)
References: UniProt: Q12690
#18: Polypeptide(L)60S ribosomal protein L14-A / 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)
References: UniProt: P36105
#19: Polypeptide(L)60S ribosomal protein L15-A / 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)
References: UniProt: P05748
#20: Polypeptide(L)60S ribosomal protein L16-A / 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)
References: UniProt: P26784
#21: Polypeptide(L)60S ribosomal protein L17-A / 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)
References: UniProt: P05740
#22: Polypeptide(L)60S ribosomal protein L18-A / 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)
References: UniProt: P0CX49
#23: Polypeptide(L)60S ribosomal protein L20-A / 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)
References: UniProt: P0CX23
#24: Polypeptide(L)60S ribosomal protein L26-A / 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)
References: UniProt: P05743

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

#5: Polypeptide(L)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)
References: UniProt: P53136
#6: Polypeptide(L)Ribosome biogenesis protein BRX1


Mass: 33585.414 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q08235
#30: Polypeptide(L)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)
References: UniProt: P53927
#31: Polypeptide(L)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)
References: UniProt: P40693
#33: Polypeptide(L)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)
References: UniProt: Q04660

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RNA chain , 1 types, 1 molecules 1

#25: RNA chain25S ribosomal RNA


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

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

#26: RNA chain5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: GenBank: 1214879358
#32: RNA chain5.8S ribosomal RNA


Mass: 74308.391 Da / Num. of mol.: 1 / Details: Backbone model
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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

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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
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 FIELD / 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 / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 10 / Used frames/image: 1-6

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Processing

EM software
IDNameVersionCategoryImage processing ID
1GautomatchPARTICLE SELECTION1
4GctfCTF CORRECTION1
9RELION2.0INITIAL EULER ASSIGNMENT1
10RELION2.0FINAL EULER ASSIGNMENT1
11RELION2.0CLASSIFICATION1
12RELION2.0RECONSTRUCTION1
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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