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- PDB-6i7o: The structure of a di-ribosome (disome) as a unit for RQC and NGD... -

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Entry
Database: PDB / ID: 6i7o
TitleThe structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • A/P hybrid tRNA
  • E-site tRNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • P-site tRNA
  • P/E hybrid tRNA
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
  • mRNAMessenger RNA
KeywordsTRANSLATION / ribosome / disome / di-ribosome / stalling
Function / homologyInsertion domain in 60S ribosomal protein L10P / Ribosomal protein S13/S18 / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 ...Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S13/S18 / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein L10 / Ribosomal protein S11 / Ribosomal protein S19e / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal L40e family / Ribosomal protein S6e / Ubiquitin family / S4 domain / Plectin/S10 domain / S25 ribosomal protein / Ribosomal protein L14 / Ribosomal protein L37e / Ribosomal L38e protein family / Ribosomal L37ae protein family / Ribosomal L29e protein family / Ribosomal L27e protein family / Ribosomal L22e protein family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S27 / Ribosomal protein L32 / Ribosomal protein S27a / Ribosomal protein L13e / Ribosomal protein L21e / Ribosomal protein S26e / Ribosomal protein S24e / Ribosomal protein L19e / Ribosomal protein S7e / Ribosomal protein S21e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L35Ae / Ribosomal protein L24e / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L23, N-terminal domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S10 domain superfamily / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 60S acidic ribosomal protein P0 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S7 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L22p/L17e
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.3 Å resolution
AuthorsTesina, P. / Cheng, J. / Becker, T. / Beckmann, R.
CitationJournal: EMBO J. / Year: 2019
Title: Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways.
Authors: Ken Ikeuchi / Petr Tesina / Yoshitaka Matsuo / Takato Sugiyama / Jingdong Cheng / Yasushi Saeki / Keiji Tanaka / Thomas Becker / Roland Beckmann / Toshifumi Inada
Abstract: Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ...Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD) can occur in a Not4-dependent manner.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2018 / Release: Jan 16, 2019

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Structure visualization

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  • EMDB-4427
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Assembly

Deposited unit
BQ: 25S ribosomal RNA
BR: 5S ribosomal RNA
BS: 5.8S ribosomal RNA
AW: 60S ribosomal protein L2-A
BA: 60S ribosomal protein L3
BE: 60S ribosomal protein L4-A
BI: 60S ribosomal protein L5
BM: 60S ribosomal protein L6-A
BO: 60S ribosomal protein L7-A
AA: 60S ribosomal protein L8-A
AD: 60S ribosomal protein L9-A
BD: 60S ribosomal protein L10
AG: 60S ribosomal protein L11-B
AJ: 60S ribosomal protein L13-A
AM: 60S ribosomal protein L14-A
AQ: 60S ribosomal protein L15-A
AU: 60S ribosomal protein L16-A
2: 18S ribosomal RNA
P: 40S ribosomal protein S0-A
Q: 40S ribosomal protein S1-A
R: 40S ribosomal protein S2
A: 40S ribosomal protein S3
S: 40S ribosomal protein S4-A
B: 40S ribosomal protein S5
T: 40S ribosomal protein S6-A
U: 40S ribosomal protein S7-A
V: 40S ribosomal protein S8-A
W: 40S ribosomal protein S9-A
C: 40S ribosomal protein S10-A
X: 40S ribosomal protein S11-A
D: 40S ribosomal protein S12
Y: 40S ribosomal protein S13
Z: 40S ribosomal protein S14-B
E: 40S ribosomal protein S15
F: 40S ribosomal protein S16-A
G: 40S ribosomal protein S17-A
H: 40S ribosomal protein S18-A
I: 40S ribosomal protein S19-A
J: 40S ribosomal protein S20
a: 40S ribosomal protein S21-A
b: 40S ribosomal protein S22-A
c: 40S ribosomal protein S23-A
d: 40S ribosomal protein S24-A
K: 40S ribosomal protein S25-A
e: 40S ribosomal protein S26-B
f: 40S ribosomal protein S27-A
L: 40S ribosomal protein S28-A
M: 40S ribosomal protein S29-A
g: 40S ribosomal protein S30-A
N: Ubiquitin-40S ribosomal protein S31
O: Guanine nucleotide-binding protein subunit beta-like protein
AX: 60S ribosomal protein L17-A
BB: 60S ribosomal protein L18-A
BF: 60S ribosomal protein L19-A
BH: 60S ribosomal protein L20-A
BJ: 60S ribosomal protein L21-A
BL: 60S ribosomal protein L22-A
AB: 60S ribosomal protein L23-A
AE: 60S ribosomal protein L24-A
AH: 60S ribosomal protein L25
AK: 60S ribosomal protein L26-A
AN: 60S ribosomal protein L27-A
AR: 60S ribosomal protein L28
AV: 60S ribosomal protein L29
AY: 60S ribosomal protein L30
BC: 60S ribosomal protein L31-A
BG: 60S ribosomal protein L32
BK: 60S ribosomal protein L33-A
BN: 60S ribosomal protein L34-A
BP: 60S ribosomal protein L35-A
AC: 60S ribosomal protein L36-A
AF: 60S ribosomal protein L37-A
AI: 60S ribosomal protein L38
AL: 60S ribosomal protein L39
AO: Ubiquitin-60S ribosomal protein L40
AS: 60S ribosomal protein L41-B
AP: 60S ribosomal protein L42-A
AT: 60S ribosomal protein L43-A
BU: 60S acidic ribosomal protein P0
2b: 18S ribosomal RNA
Pb: 40S ribosomal protein S0-A
Qb: 40S ribosomal protein S1-A
Rb: 40S ribosomal protein S2
Ab: 40S ribosomal protein S3
Sb: 40S ribosomal protein S4-A
Bb: 40S ribosomal protein S5
Tb: 40S ribosomal protein S6-A
Ub: 40S ribosomal protein S7-A
Vb: 40S ribosomal protein S8-A
Wb: 40S ribosomal protein S9-A
Cb: 40S ribosomal protein S10-A
Xb: 40S ribosomal protein S11-A
Db: 40S ribosomal protein S12
Yb: 40S ribosomal protein S13
Zb: 40S ribosomal protein S14-B
Eb: 40S ribosomal protein S15
Fb: 40S ribosomal protein S16-A
Gb: 40S ribosomal protein S17-A
Hb: 40S ribosomal protein S18-A
Ib: 40S ribosomal protein S19-A
Jb: 40S ribosomal protein S20
ab: 40S ribosomal protein S21-A
bb: 40S ribosomal protein S22-A
cb: 40S ribosomal protein S23-A
db: 40S ribosomal protein S24-A
Kb: 40S ribosomal protein S25-A
eb: 40S ribosomal protein S26-B
fb: 40S ribosomal protein S27-A
Lb: 40S ribosomal protein S28-A
Mb: 40S ribosomal protein S29-A
gb: 40S ribosomal protein S30-A
Nb: Ubiquitin-40S ribosomal protein S31
Ob: Guanine nucleotide-binding protein subunit beta-like protein
YQ: 25S ribosomal RNA
YR: 5S ribosomal RNA
YS: 5.8S ribosomal RNA
XW: 60S ribosomal protein L2-A
YA: 60S ribosomal protein L3
YE: 60S ribosomal protein L4-A
YI: 60S ribosomal protein L5
YM: 60S ribosomal protein L6-A
YO: 60S ribosomal protein L7-A
XA: 60S ribosomal protein L8-A
XD: 60S ribosomal protein L9-A
YD: 60S ribosomal protein L10
XG: 60S ribosomal protein L11-B
XJ: 60S ribosomal protein L13-A
XM: 60S ribosomal protein L14-A
XQ: 60S ribosomal protein L15-A
XU: 60S ribosomal protein L16-A
XX: 60S ribosomal protein L17-A
YB: 60S ribosomal protein L18-A
YF: 60S ribosomal protein L19-A
YH: 60S ribosomal protein L20-A
YJ: 60S ribosomal protein L21-A
YL: 60S ribosomal protein L22-A
XB: 60S ribosomal protein L23-A
XE: 60S ribosomal protein L24-A
XH: 60S ribosomal protein L25
XK: 60S ribosomal protein L26-A
XN: 60S ribosomal protein L27-A
XR: 60S ribosomal protein L28
XV: 60S ribosomal protein L29
XY: 60S ribosomal protein L30
YC: 60S ribosomal protein L31-A
YG: 60S ribosomal protein L32
YK: 60S ribosomal protein L33-A
YN: 60S ribosomal protein L34-A
YP: 60S ribosomal protein L35-A
XC: 60S ribosomal protein L36-A
XF: 60S ribosomal protein L37-A
XI: 60S ribosomal protein L38
XL: 60S ribosomal protein L39
XO: Ubiquitin-60S ribosomal protein L40
XS: 60S ribosomal protein L41-B
XP: 60S ribosomal protein L42-A
XT: 60S ribosomal protein L43-A
YU: 60S acidic ribosomal protein P0
n: P-site tRNA
m: E-site tRNA
nb: A/P hybrid tRNA
mb: P/E hybrid tRNA
l: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,232,474178
Polyers6,231,493163
Non-polymers98115
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 9 types, 13 molecules BQYQBRYRBSYS22bnmnbmbl

#1: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#2: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1329886537
#3: RNA chain 5.8S ribosomal RNA /


Mass: 50376.758 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1489318609
#18: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 874346701
#80: RNA chain P-site tRNA


Mass: 24468.551 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1329886529
#81: RNA chain E-site tRNA


Mass: 24004.262 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 176418
#82: RNA chain A/P hybrid tRNA


Mass: 24501.539 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#83: RNA chain P/E hybrid tRNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#84: RNA chain mRNA / Messenger RNA


Mass: 17904.270 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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60S ribosomal protein ... , 40 types, 80 molecules AWXWBAYABEYEBIYIBMYMBOYOAAXAADXDBDYDAGXGAJXJAMXMAQXQAUXUAXXX...

#4: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#5: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#6: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#7: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33415.387 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#8: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#9: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 25341.480 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#10: 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: 25656.840 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#11: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21491.902 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#12: Protein/peptide 60S ribosomal protein L10 / / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41805
#13: Protein/peptide 60S ribosomal protein L11-B / Ribosome / L16 / Large ribosomal subunit protein uL5-B / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E757
#14: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 21956.312 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#15: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15063.870 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#16: Protein/peptide 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#17: Protein/peptide 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#52: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#53: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#54: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#55: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#56: Protein/peptide 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#57: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11006.555 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#58: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14218.625 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#59: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 15506.229 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#60: Protein/peptide 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 13641.997 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#61: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 13892.317 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#62: Protein/peptide 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#63: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#64: Protein/peptide 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6560.688 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#65: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 10902.664 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#66: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#67: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14478.054 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#68: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#69: Protein/peptide 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#70: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#71: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#72: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9300.709 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#73: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8714.363 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#74: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#76: Protein/peptide 60S ribosomal protein L41-B / Ribosome / L47 / Large ribosomal subunit protein eL41-B / YL41


Mass: 3354.243 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX87
#77: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX27
#78: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25

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40S ribosomal protein ... , 31 types, 62 molecules PPbQQbRRbAAbSSbBBbTTbUUbVVbWWbCCbXXbDDbYYbZZb...

#19: Protein/peptide 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 22811.074 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32905
#20: Protein/peptide 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 24498.365 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33442
#21: Protein/peptide 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 23212.979 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25443
#22: Protein/peptide 40S ribosomal protein S3 / / RP13 / Small ribosomal subunit protein uS3 / YS3


Mass: 24702.791 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05750
#23: Protein/peptide 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29338.133 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX35
#24: Protein/peptide 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 22908.338 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26783
#25: Protein/peptide 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 24965.975 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX37
#26: Protein/peptide 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21071.570 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26786
#27: Protein/peptide 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX39
#28: Protein/peptide 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 21210.662 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: O13516
#29: Protein/peptide 40S ribosomal protein S10-A / Ribosome / Small ribosomal subunit protein eS10-A


Mass: 11042.562 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08745
#30: Protein/peptide 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 16588.461 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX47
#31: Protein/peptide 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 13327.331 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P48589
#32: Protein/peptide 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05756
#33: Protein/peptide 40S ribosomal protein S14-B / Ribosome / RP59B / Small ribosomal subunit protein uS11-B


Mass: 13560.528 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39516
#34: Protein/peptide 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 13421.732 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q01855
#35: Protein/peptide 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15659.216 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX51
#36: Protein/peptide 40S ribosomal protein S17-A / Ribosome / RP51A / Small ribosomal subunit protein eS17-A


Mass: 14268.545 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02407
#37: Protein/peptide 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX55
#38: Protein/peptide 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P07280
#39: Protein/peptide 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 11476.479 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38701
#40: Protein/peptide 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0V8
#41: Protein/peptide 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W1
#42: Protein/peptide 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX29
#43: Protein/peptide 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX31
#44: Protein/peptide 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 7930.299 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E792
#45: Protein/peptide 40S ribosomal protein S26-B / Ribosome / Small ribosomal subunit protein eS26-B


Mass: 11022.989 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39939
#46: Protein/peptide 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35997
#47: Protein/peptide 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q3E7X9
#48: Protein/peptide 40S ribosomal protein S29-A / Ribosome / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6335.303 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41057
#49: Protein/peptide 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 6779.086 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX33

-
Protein/peptide , 4 types, 8 molecules NNbOObAOXOBUYU

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


Mass: 8329.946 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05759
#51: Protein/peptide Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34151.426 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38011
#75: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CH08
#79: Protein/peptide 60S acidic ribosomal protein P0 / A0 / L10e / Large ribosomal subunit protein uL10


Mass: 33749.121 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05317

-
Non-polymers , 1 types, 15 molecules

#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Formula: Zn / Zinc

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of a native stalled di-ribosome (disome) complex from S. cerevisiae
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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15739 / Symmetry type: POINT

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