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- PDB-6hcm: Structure of the rabbit collided di-ribosome (stalled monosome) -

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Entry
Database: PDB / ID: 6hcm
TitleStructure of the rabbit collided di-ribosome (stalled monosome)
Components
  • (40S ribosomal protein ...) x 6
  • (60S ribosomal protein ...) x 4
  • (Ribosomal protein ...) x 15
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • ATP binding cassette subfamily E member 1
  • P-site tRNA
  • RACK1Receptor for activated C kinase 1
  • Ribosomal protein
  • eL13
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL8
  • eRF1(AAQ)
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS4
  • eS8
  • mRNAMessenger RNA
  • nascent chain
  • uL10
  • uL13
  • uL15
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS19
  • uS2
  • uS3
  • uS5
KeywordsRIBOSOME / Translation / Quality Control / Ribosome
Function / homologyRibosomal protein L11, conserved site / RLI, domain 1 / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily ...Ribosomal protein L11, conserved site / RLI, domain 1 / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L30/YlxQ / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S4/S9 N-terminal domain / 4Fe-4S binding domain / ABC transporter / Ubiquitin-like protein FUBI / Ribosomal protein L35A superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L24e/L24 superfamily / S27a-like superfamily / Ribosomal protein L36e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L16p/L10e / Ribosomal protein S6e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S3Ae, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S3, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L15e core domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.8 Å resolution
AuthorsJuszkiewicz, S. / Chandrasekaran, V. / Lin, Z. / Kraatz, S. / Ramakrishnan, V. / Hegde, R.S.
CitationJournal: Mol. Cell / Year: 2018
Title: ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
Authors: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde
Abstract: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 15, 2018 / Release: Oct 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 17, 2018Structure modelrepositoryInitial release
1.1Nov 14, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A1: 18S ribosomal RNA
B1: uS2
C1: 40S ribosomal protein S3a
D1: uS5
E1: uS3
F1: eS4
G1: Ribosomal protein S5
H1: 40S ribosomal protein S6
I1: 40S ribosomal protein S7
J1: eS8
K1: Ribosomal protein S9 (Predicted)
L1: eS10
M1: Ribosomal protein S11
N1: 40S ribosomal protein S12
O1: uS15
P1: uS11
Q1: uS19
R1: Ribosomal protein S16
S1: eS17
T1: uS13
U1: eS19
V1: uS10
W1: eS21
X1: Ribosomal protein S15a
Y1: uS12
Z1: eS24
a1: eS25
b1: eS26
c1: 40S ribosomal protein S27
d1: Ribosomal protein S28
e1: uS14
f1: 40S ribosomal protein S30
g1: Ribosomal protein S27a
h1: RACK1
j1: eRF1(AAQ)
k1: ATP binding cassette subfamily E member 1
52: 28S ribosomal RNA
72: 5S ribosomal RNA
82: 5.8S ribosomal RNA
A3: Ribosomal protein L8
B3: uL3
C3: uL4
E3: 60S ribosomal protein L6
F3: uL30
H3: uL6
L3: eL13
M3: Ribosomal protein L14
N3: Ribosomal protein L15
O3: uL13
P3: uL22
Q3: eL18
R3: eL19
S3: eL20
T3: eL21
U3: eL22
V3: Ribosomal protein L23
W3: eL24
X3: uL23
Y3: Ribosomal protein L26
Z3: eL27
a3: uL15
b3: eL29
c3: eL30
d3: eL31
e3: eL32
f3: eL33
g3: eL34
h3: uL29
i3: 60S ribosomal protein L36
j3: Ribosomal protein L37
k3: eL38
l3: eL39
m3: eL40
n3: eL41
o3: eL42
p3: eL43
r3: eL28
s3: uL10
t3: Ribosomal protein L12
23: P-site tRNA
w3: mRNA
J3: Ribosomal protein L11
G3: eL8
D3: 60S ribosomal protein L5
I3: 60S ribosomal protein L10
1: nascent chain
u3: Ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,574,213397
Polyers3,565,69587
Non-polymers8,518310
Water724
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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RNA chain , 6 types, 6 molecules A152728223w3

#1: RNA chain 18S ribosomal RNA /


Mass: 602778.875 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: RNA chain 28S ribosomal RNA /


Mass: 1177577.000 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: RNA chain P-site tRNA


Mass: 24436.551 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: RNA chain mRNA / Messenger RNA


Mass: 7387.504 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein/peptide , 56 types, 56 molecules B1D1E1F1J1L1O1P1Q1S1T1U1V1W1Y1Z1a1b1e1h1j1k1B3C3F3H3L3O3P3Q3...

#2: Protein/peptide uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein/peptide uS5


Mass: 31327.395 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein/peptide uS3


Mass: 26715.344 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#6: Protein/peptide eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein/peptide eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein/peptide eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#15: Protein/peptide uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#16: Protein/peptide uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein/peptide uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#19: Protein/peptide eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein/peptide uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#21: Protein/peptide eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein/peptide uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#23: Protein/peptide eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein/peptide uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein/peptide eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein/peptide eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#28: Protein/peptide eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein/peptide uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#34: Protein/peptide RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#35: Protein/peptide eRF1(AAQ)


Mass: 49264.926 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein/peptide ATP binding cassette subfamily E member 1


Mass: 67405.234 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SG72
#41: Protein/peptide uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#42: Protein/peptide uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein/peptide uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#45: Protein/peptide uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33
#46: Protein/peptide eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein/peptide uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein/peptide uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#51: Protein/peptide eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein/peptide eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein/peptide eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein/peptide eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#55: Protein/peptide eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein/peptide eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#58: Protein/peptide uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#60: Protein/peptide eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#61: Protein/peptide uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein/peptide eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein/peptide eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#64: Protein/peptide eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#65: Protein/peptide eL32 / CD59


Mass: 15767.736 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#66: Protein/peptide eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#67: Protein/peptide eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein/peptide uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#71: Protein/peptide eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein/peptide eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#73: Protein/peptide eL40


Mass: 11699.790 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#74: Protein/peptide eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein/peptide eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein/peptide eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#77: Protein/peptide eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#78: Protein/peptide uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: Protein/peptide eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#86: Protein/peptide nascent chain


Mass: 1581.727 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit)
#87: Protein/peptide Ribosomal protein /


Mass: 24879.422 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

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40S ribosomal protein ... , 6 types, 6 molecules C1H1I1N1c1f1

#3: Protein/peptide 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#8: Protein/peptide 40S ribosomal protein S6 /


Mass: 28751.906 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#9: Protein/peptide 40S ribosomal protein S7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#14: Protein/peptide 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#29: Protein/peptide 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#32: Protein/peptide 40S ribosomal protein S30 /


Mass: 14498.884 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2

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Ribosomal protein ... , 15 types, 15 molecules G1K1M1R1X1d1g1A3M3N3V3Y3j3t3J3

#7: Protein/peptide Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#11: Protein/peptide Ribosomal protein S9 (Predicted) / Ribosome


Mass: 22641.564 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#13: Protein/peptide Ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#18: Protein/peptide Ribosomal protein S16 /


Mass: 16477.377 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#24: Protein/peptide Ribosomal protein S15a / Ribosome


Mass: 14865.555 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#30: Protein/peptide Ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#33: Protein/peptide Ribosomal protein S27a / Ribosome


Mass: 18004.041 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#40: Protein/peptide Ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#47: Protein/peptide Ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#48: Protein/peptide Ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#56: Protein/peptide Ribosomal protein L23 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#59: Protein/peptide Ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#70: Protein/peptide Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#79: Protein/peptide Ribosomal protein L12 /


Mass: 17847.619 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#82: Protein/peptide Ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8

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60S ribosomal protein ... , 4 types, 4 molecules E3i3D3I3

#43: Protein/peptide 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#69: Protein/peptide 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#84: Protein/peptide 60S ribosomal protein L5 /


Mass: 34481.828 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#85: Protein/peptide 60S ribosomal protein L10 / / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2

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Non-polymers , 4 types, 314 molecules

#88: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 300 / Formula: Mg / Magnesium
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#90: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4 / Iron–sulfur cluster
#91: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Formula: H2O / Water

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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: Rabbit 80S stalled on globin mRNA at the stop codon / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87
Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
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: 1.79 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 14634 / Symmetry type: POINT

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