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- PDB-6eml: Cryo-EM structure of a late pre-40S ribosomal subunit from Saccha... -

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Entry
Database: PDB / ID: 6eml
TitleCryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae
Components
  • (40S ribosomal protein ...) x 26
  • Essential nuclear protein 1
  • Pre-rRNA-processing protein PNO1
  • Ribosome biogenesis protein TSR1
  • Serine/threonine-protein kinase RIO2
  • Ubiquitin-40S ribosomal protein S31
  • pre-18S ribosomal RNA
KeywordsRIBOSOME / ribosome / biogenesis / small subunit / 40S
Function / homologyRIO1 family / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / S4 domain / Ribosomal protein S27a / Ribosomal protein S27 ...RIO1 family / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / S4 domain / Ribosomal protein S27a / Ribosomal protein S27 / S25 ribosomal protein / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Bystin / RS4NT (NUC023) domain / Ribosomal protein S6e / AARP2CN (NUC121) domain / Rio2, N-terminal / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S28e / Ribosomal protein S19e / Ribosomal protein S6e signature. / Ribosomal protein S4e, central domain superfamily / Bms1/Tsr1-type G domain / Serine/threonine-protein kinase Rio2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S19e domain superfamily / S27a-like superfamily / Ribosomal S3Ae family / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal protein S24e signature. / Ribosomal protein S5 signature. / 50S ribosomal protein L30e-like / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / rt:r-sce-69229: / Formation of a pool of free 40S subunits / UCH proteinases / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Protein methylation / Peroxisomal protein import / Iron uptake and transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / Ribosomal protein S2 / Krr1 KH1 domain / Ub-specific processing proteases / MAPK6/MAPK4 signaling / Ribosomal protein S19e signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsHeuer, A. / Thomson, E. / Schmidt, C. / Berninghausen, O. / Becker, T. / Hurt, E. / Beckmann, R.
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of a late pre-40S ribosomal subunit from .
Authors: André Heuer / Emma Thomson / Christian Schmidt / Otto Berninghausen / Thomas Becker / Ed Hurt / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 2, 2017 / Release: Nov 29, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 29, 2017Structure modelrepositoryInitial release
1.1Feb 21, 2018Structure modelDatabase referencescitation_citation.title
1.2Mar 28, 2018Structure modelData collection / Database referencescitation_citation.title

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Structure visualization

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Assembly

Deposited unit
2: pre-18S ribosomal RNA
D: 40S ribosomal protein S12
B: 40S ribosomal protein S5
C: 40S ribosomal protein S17-A
E: 40S ribosomal protein S15
F: 40S ribosomal protein S16-A
H: 40S ribosomal protein S18-A
I: 40S ribosomal protein S19-A
K: 40S ribosomal protein S25-A
L: 40S ribosomal protein S28-B
N: Ubiquitin-40S ribosomal protein S31
P: 40S ribosomal protein S0-A
Q: 40S ribosomal protein S1-A
R: 40S ribosomal protein S2
S: 40S ribosomal protein S4-A
T: 40S ribosomal protein S6-A
U: 40S ribosomal protein S7-A
V: 40S ribosomal protein S8-A
W: 40S ribosomal protein S9-A
X: 40S ribosomal protein S11-A
Y: 40S ribosomal protein S13
Z: 40S ribosomal protein S14-A
a: 40S ribosomal protein S21-A
b: 40S ribosomal protein S22-A
c: 40S ribosomal protein S23-A
d: 40S ribosomal protein S24-A
f: 40S ribosomal protein S27-A
t: Ribosome biogenesis protein TSR1
g: 40S ribosomal protein S30-A
p: Pre-rRNA-processing protein PNO1
r: Serine/threonine-protein kinase RIO2
e: Essential nuclear protein 1


Theoretical massNumber of molelcules
Total (without water)1,292,45832
Polyers1,292,45832
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)160050
ΔGint (kcal/M)-1149
Surface area (Å2)418910
MethodPISA

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain pre-18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132

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40S ribosomal protein ... , 26 types, 26 molecules DBCEFHIKLPQRSTUVWXYZabcdfg

#2: Protein/peptide 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 15488.631 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48589
#3: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 25072.600 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#4: Protein/peptide 40S ribosomal protein S17-A / Ribosome / RP51A / Small ribosomal subunit protein eS17-A


Mass: 15820.413 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02407
#5: Protein/peptide 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 16031.907 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01855
#6: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15877.490 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#7: Protein/peptide 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#8: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07280
#9: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 12067.272 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E792
#10: Protein/peptide 40S ribosomal protein S28-B / Ribosome / S33 / Small ribosomal subunit protein eS28-B / YS27


Mass: 7578.822 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0X0
#12: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28051.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32905
#13: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 28798.467 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#14: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 27490.826 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25443
#15: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29469.330 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#16: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 27054.486 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#17: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21658.209 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#18: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#19: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#20: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 17785.934 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#21: Protein/peptide 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#22: Protein/peptide 40S ribosomal protein S14-A / Ribosome / RP59A / Small ribosomal subunit protein uS11-A


Mass: 14562.655 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06367
#23: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0V8
#24: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#25: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 16073.896 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#26: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15362.848 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#27: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#29: Protein/peptide 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX33

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Protein/peptide , 5 types, 5 molecules Ntpre

#11: Protein/peptide Ubiquitin-40S ribosomal protein S31


Mass: 17254.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05759
#28: Protein/peptide Ribosome biogenesis protein TSR1 / / 20S rRNA accumulation protein 1


Mass: 90876.539 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07381
#30: Protein/peptide Pre-rRNA-processing protein PNO1 / Partner of NOB1 / Ribosomal RNA-processing protein 20


Mass: 30380.623 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99216
#31: Protein/peptide Serine/threonine-protein kinase RIO2


Mass: 49192.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P40160, non-specific serine/threonine protein kinase
#32: Protein/peptide Essential nuclear protein 1


Mass: 55207.422 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38333

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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: late pre-40S ribosomal subunit / Type: RIBOSOME
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
Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
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
VitrificationCryogen 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
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: EM-Tools / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 84100 / Symmetry type: POINT

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