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- PDB-6sgc: Rabbit 80S ribosome stalled on a poly(A) tail -

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Entry
Database: PDB / ID: 6sgc
TitleRabbit 80S ribosome stalled on a poly(A) tail
Components
  • (40S ribosomal protein ...) x 8
  • (60S ribosomal protein ...) x 6
  • (Ribosomal protein ...) x 15
  • (uS5) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosomal protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • Ribosomal_L28e domain-containing protein
  • Ribosomal_L7Ae domain-containing protein
  • Ribosomal_S10 domain-containing protein
  • Ribosomal_S13_N domain-containing protein
  • S10_plectin domain-ontaining protein
  • TRASH domain-containing protein
  • WD_REPEATS_REGION domain-containing protein
  • eL13
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL29
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL42
  • eL43
  • eL8
  • eS13
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • poly-lysine nascent chain
  • polyA mRNA
  • tRNA (Lys3)
  • uL10
  • uL13
  • uL22
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS11
  • uS12
  • uS14
  • uS19
  • uS2
KeywordsRIBOSOME / Protein Translation / Ribosome Stalling / polyA tail
Function / homology
Function and homology information


regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / cytosolic ribosome / DNA-(apurinic or apyrimidinic site) lyase / TOR signaling / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / polysomal ribosome ...regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / cytosolic ribosome / DNA-(apurinic or apyrimidinic site) lyase / TOR signaling / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / polysomal ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of translation / cytoplasmic ribonucleoprotein granule / mRNA 5'-UTR binding / positive regulation of protein-containing complex assembly / rRNA processing / cellular response to gamma radiation / cytoplasmic translation / cell body / cytosolic large ribosomal subunit / large ribosomal subunit / cytosolic small ribosomal subunit / 5S rRNA binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / small ribosomal subunit / ribonucleoprotein complex / ribosome / rRNA binding / structural constituent of ribosome / cell differentiation / positive regulation of NF-kappaB transcription factor activity / postsynaptic density / translation / synapse / positive regulation of apoptotic process / dendrite / nucleolus / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / cytoplasm
Ribosomal protein L11, N-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5, N-terminal ...Ribosomal protein L11, N-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5, N-terminal / Winged helix DNA-binding domain superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L22/L17 superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L38e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein L36e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S10 domain / S27a-like superfamily / Ribosomal protein L31e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L15e, conserved site / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L5, conserved site / 30s ribosomal protein S13, C-terminal / Ribosomal protein S19, superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e/L15P / Ribosomal protein L34Ae superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S6e, conserved site / Ribosomal protein S19e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L23 / Ribosomal protein S8 / Ribosomal protein L24e / Ribosomal protein L14p/L23e / Ribosomal protein S10p/S20e / Ribosomal protein L21e / S25 ribosomal protein / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal protein S9/S16 / Ribosomal protein S19 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S15 / Ribosomal L15 / Ribosomal L27e protein family
40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 60S ribosomal protein L23 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L41 / 60S ribosomal protein L31 / Uncharacterized protein ...40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 60S ribosomal protein L23 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L41 / 60S ribosomal protein L31 / Uncharacterized protein / 60S ribosomal protein L21 / 40S ribosomal protein S30 / 40S ribosomal protein S18 / 60S ribosomal protein L17 / 60S ribosomal protein L11 / Uncharacterized protein / 40S ribosomal protein S17 / 60S ribosomal protein L36 / Uncharacterized protein / 60S ribosomal protein L8 / 40S ribosomal protein S11 / S10_plectin domain-containing protein / 40S ribosomal protein S3 / 60S ribosomal protein L27 / 40S ribosomal protein S19 / 40S ribosomal protein S6 / Uncharacterized protein / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 40S ribosomal protein S28 / 40S ribosomal protein S15a / Ribosomal protein S5 / 60S ribosomal protein L30 / 40S ribosomal protein S25 / 60S ribosomal protein L9 / 40S ribosomal protein S27 / 60S ribosomal protein L35 / 60S ribosomal protein L9 / 40S ribosomal protein S20 / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S27a / 60S ribosomal protein L6 / 60S ribosomal protein L12 / 60S ribosomal protein L27a / 40S ribosomal protein S13 / Ribosomal protein L26 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / Uncharacterized protein / 60S ribosomal protein L38 / Ribosomal_L18_c domain-containing protein / 60S ribosomal protein L14 / Ribosomal protein L15 / Ribosomal protein L37 / 60S ribosomal protein L34 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / Ribosomal protein L32 / Uncharacterized protein / 40S ribosomal protein S15 / Ribosomal protein
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChandrasekaran, V. / Juszkiewicz, S. / Choi, J. / Puglisi, J.D. / Brown, A. / Shao, S. / Ramakrishnan, V. / Hegde, R.S.
Funding support United Kingdom, United States, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A022_1007 United Kingdom
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
National Institutes of Health/National Institute of General Medical SciencesGM51266 United States
National Institutes of Health/National Institute of General Medical SciencesGM113078 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Mechanism of ribosome stalling during translation of a poly(A) tail.
Authors: Viswanathan Chandrasekaran / Szymon Juszkiewicz / Junhong Choi / Joseph D Puglisi / Alan Brown / Sichen Shao / V Ramakrishnan / Ramanujan S Hegde /
Abstract: Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. ...Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A1: 18S ribosomal RNA
B1: uS2
C1: 40S ribosomal protein S3a
D1: uS5
E1: uS5
F1: 40S ribosomal protein S4
G1: Ribosomal protein S5
H1: 40S ribosomal protein S6
I1: 40S ribosomal protein S7
J1: 40S ribosomal protein S8
K1: Ribosomal protein S9 (Predicted)
L1: S10_plectin domain-ontaining protein
M1: Ribosomal protein S11
N1: 40S ribosomal protein S12
O1: Ribosomal_S13_N domain-containing protein
P1: uS11
Q1: uS19
R1: Ribosomal protein S16
S1: eS17
T1: eS13
U1: eS19
V1: Ribosomal_S10 domain-containing protein
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: WD_REPEATS_REGION domain-containing protein
i1: polyA mRNA
A2: Ribosomal protein L8
B2: uL3
C2: uL4
D2: 60S ribosomal protein L5
E2: 60S ribosomal protein L6
F2: uL30
G2: eL8
H2: uL6
I2: 60S ribosomal protein L10
J2: Ribosomal protein L11
L2: eL13
M2: Ribosomal protein L14
N2: Ribosomal protein L15
O2: uL13
P2: uL22
Q2: eL18
R2: eL19
S2: eL20
T2: eL21
U2: eL22
V2: Ribosomal protein L23
W2: TRASH domain-containing protein
X2: Ribosomal_L23eN domain-containing protein
Y2: Ribosomal protein L26
Z2: 60S ribosomal protein L27
a2: Ribosomal_L18e/L15P domain-containing protein
b2: eL29
c2: Ribosomal_L7Ae domain-containing protein
d2: eL31
e2: eL32
f2: eL33
g2: eL34
h2: uL29
i2: 60S ribosomal protein L36
j2: Ribosomal protein L37
k2: eL38
l2: eL39
m2: eL40
n2: 60s ribosomal protein l41
o2: eL42
p2: eL43
r2: Ribosomal_L28e domain-containing protein
s2: uL10
t2: Ribosomal protein L12
54: 28S ribosomal RNA
74: 5S ribosomal RNA
84: 5.8S ribosomal RNA
XX: poly-lysine nascent chain
B: Ribosomal protein
23: tRNA (Lys3)
33: tRNA (Lys3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,468,048371
Polymers3,460,55086
Non-polymers7,498285
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 7 molecules A1i15474842333

#1: RNA chain 18S ribosomal RNA /


Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: RNA chain polyA mRNA


Mass: 3247.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Salmonella virus SP6 (bacteriophage)
#80: RNA chain 28S ribosomal RNA /


Mass: 1167622.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: RNA chain tRNA (Lys3)


Mass: 24776.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 49 types, 49 molecules B1D1E1L1O1P1Q1S1T1U1V1W1Y1Z1a1b1e1h1B2C2F2G2H2L2O2P2Q2R2S2T2...

#2: Protein uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein uS5


Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein uS5


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#12: Protein S10_plectin domain-ontaining protein


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#15: Protein Ribosomal_S13_N domain-containing protein


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


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein uS19


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


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein eS13


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


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#22: Protein Ribosomal_S10 domain-containing protein


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


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein eS25


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


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#34: Protein WD_REPEATS_REGION domain-containing protein


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#37: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#38: Protein uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#42: Protein eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#46: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein uL22


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


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein eL21 /


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


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein TRASH domain-containing protein


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#58: Protein Ribosomal_L23eN domain-containing protein


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#61: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#62: Protein eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein Ribosomal_L7Ae domain-containing protein


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


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


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#66: Protein eL33


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


Mass: 13196.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#68: Protein uL29


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


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#72: Protein eL39


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


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#76: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#77: Protein Ribosomal_L28e domain-containing protein


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


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein Ribosomal protein /


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

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40S ribosomal protein ... , 8 types, 8 molecules C1F1H1I1J1N1c1f1

#3: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#6: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#8: Protein 40S ribosomal protein S6 /


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


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#10: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#14: Protein 40S ribosomal protein S12 /


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


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


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

+
Ribosomal protein ... , 15 types, 15 molecules G1K1M1R1X1d1g1A2J2M2N2V2Y2j2t2

#7: Protein Ribosomal protein S5 /


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


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


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


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


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


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


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#36: Protein Ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#45: Protein Ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#47: Protein Ribosomal protein L14 /


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


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


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


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


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


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7

+
60S ribosomal protein ... , 6 types, 6 molecules D2E2I2Z2i2n2

#39: Protein 60S ribosomal protein L5 /


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#40: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#44: Protein 60S ribosomal protein L10 / / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#60: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#69: Protein 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#74: Protein/peptide 60s ribosomal protein l41 / / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

+
Protein/peptide , 1 types, 1 molecules XX

#83: Protein/peptide poly-lysine nascent chain


Mass: 2084.892 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

+
Non-polymers , 3 types, 285 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#88: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3

+
Details

Has ligand of interestN

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Rabbit 80S ribosome stalled on polyA mRNARIBOSOME#1-#850MULTIPLE SOURCES
2ribosomeRIBOSOME#1-#34, #36-#851NATURAL
3polyA mRNACOMPLEX#351RECOMBINANT
Molecular weightValue: 4.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Oryctolagus cuniculus (rabbit)9986
33Homo sapiens (human)9606
Source (recombinant)Organism: Salmonella virus SP6 (bacteriophage)
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector model
1141.8INTEGRATINGFEI FALCON III (4k x 4k)
2141.8FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND2CTF correction
7Coot0.8.5model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148615 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0129234885
ELECTRON MICROSCOPYf_angle_d0.8529344651
ELECTRON MICROSCOPYf_chiral_restr0.052842873
ELECTRON MICROSCOPYf_plane_restr0.005422332
ELECTRON MICROSCOPYf_dihedral_angle_d15.4273129273

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