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

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Basic information

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


oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / regulation of translation involved in cellular response to UV / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / regulation of translation involved in cellular response to UV / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / NF-kappaB complex / mammalian oogenesis stage / cytosolic ribosome / positive regulation of endodeoxyribonuclease activity / protein kinase A binding / activation-induced cell death of T cells / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / erythrocyte development / oxidized purine DNA binding / TOR signaling / T cell proliferation involved in immune response / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / spindle assembly / positive regulation of interleukin-2 production / ribosomal small subunit biogenesis / ribosomal large subunit biogenesis / positive regulation of JUN kinase activity / gastrulation / positive regulation of microtubule polymerization / polysome / polysomal ribosome / mitotic cell cycle checkpoint / Hsp70 protein binding / cellular response to leukemia inhibitory factor / endodeoxyribonuclease activity / negative regulation of protein ubiquitination / small ribosomal subunit rRNA binding / Hsp90 protein binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / mRNA 5'-UTR binding / mitotic spindle / small ribosomal subunit / chromosome segregation / positive regulation of translation / DNA damage response, detection of DNA damage / cytoplasmic ribonucleoprotein granule / cytoplasmic translation / rRNA processing / T cell differentiation in thymus / ruffle membrane / placenta development / cellular response to gamma radiation / positive regulation of NIK/NF-kappaB signaling / cell body / large ribosomal subunit / G1/S transition of mitotic cell cycle / cytosolic large ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / cellular response to hydrogen peroxide / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / viral capsid / cellular response to tumor necrosis factor / glucose homeostasis / RNA polymerase II regulatory region sequence-specific DNA binding / mitochondrial inner membrane / negative regulation of translation / ribosome / rRNA binding / microtubule binding / killing of cells of other organism / structural constituent of ribosome / antimicrobial humoral immune response mediated by antimicrobial peptide / mitochondrial matrix / postsynaptic density / positive regulation of NF-kappaB transcription factor activity / cell differentiation / translation / mRNA binding / protein-containing complex binding / defense response to Gram-negative bacterium / positive regulation of apoptotic process / dendrite / transcription factor binding / nucleolus / structural molecule activity / positive regulation of gene expression / protein kinase binding / endoplasmic reticulum / negative regulation of apoptotic process / Golgi apparatus / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Ribosomal protein L11, N-terminal domain / Ribosomal protein S7 domain / 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 / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal ...Ribosomal protein L11, N-terminal domain / Ribosomal protein S7 domain / 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 / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein L1-like / Ubiquitin-like domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L15 / Ribosomal protein L2, conserved site / Winged helix DNA-binding domain 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 S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L5, C-terminal / 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 / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L5, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21e, 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 L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L34e, conserved site / WD40-repeat-containing domain / Ribosomal protein L10e/L16 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L30, ferredoxin-like fold domain / K homology domain-like, alpha/beta / Ribosomal protein S19e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S9, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S6e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein S13/S18 / Ribosomal proteins L26 eukaryotic, L24P archaeal
Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S8 / Outer capsid protein VP2 / 40S ribosomal protein S12 / Uncharacterized protein / Ribosomal_S10 domain-containing protein / TRASH domain-containing protein / Ribosomal protein S9 (Predicted) / Ribosomal protein L10 (Predicted) ...Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S8 / Outer capsid protein VP2 / 40S ribosomal protein S12 / Uncharacterized protein / Ribosomal_S10 domain-containing protein / TRASH domain-containing protein / Ribosomal protein S9 (Predicted) / Ribosomal protein L10 (Predicted) / 60s ribosomal protein l41 / Ribosomal_L23eN domain-containing protein / Ribosomal protein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S27 / 60S ribosomal protein L27 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L36 / Ribosomal_L28e domain-containing protein / Uncharacterized protein / Ribosomal_L2_C domain-containing protein / Ribosomal_S17_N domain-containing protein / S10_plectin domain-containing protein / Uncharacterized protein / KH type-2 domain-containing protein / Uncharacterized protein / 40S ribosomal protein S6 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / 60S ribosomal protein L5 / 60S ribosomal protein L6 / 40S ribosomal protein S4 / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein / Ribosomal_S13_N domain-containing protein / KOW domain-containing protein / 40S ribosomal protein S3a / 40S ribosomal protein S7 / VP5 / Ribosomal_L14e domain-containing protein / Uncharacterized protein / Ribosomal protein L15 / Uncharacterized protein / 40S ribosomal protein S30 / 40S ribosomal protein S25 / Ribosomal_L7Ae domain-containing protein / Ribosomal_S7 domain-containing protein / Uncharacterized protein / Ribosomal protein S28 / Ribosomal protein L37 / Uncharacterized 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

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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/peptide , 50 types, 50 molecules B1D1E1L1O1P1Q1S1T1U1V1W1Y1Z1a1b1e1h1B2C2F2G2H2L2O2P2Q2R2S2T2...

#2: Protein/peptide uS2


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


Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein/peptide 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/peptide 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/peptide 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/peptide uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide eS21


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


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


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein/peptide 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/peptide eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein/peptide 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/peptide 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/peptide 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/peptide uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein/peptide 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/peptide eL8


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


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


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


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein/peptide 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/peptide eL18


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


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


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein/peptide 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/peptide eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein/peptide 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/peptide 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/peptide 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/peptide eL29


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#63: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide eL40


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein/peptide 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/peptide 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/peptide 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/peptide uL10


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

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

#3: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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

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

#7: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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

+
Non-polymers , 3 types, 285 molecules

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


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


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


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

+
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 mRNARIBOSOME1, 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, 850MULTIPLE SOURCES
2ribosomeRIBOSOME1, 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, 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, 851NATURAL
3polyA mRNACOMPLEX351RECOMBINANT
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

Imaging-ID: 1 / Electron dose: 41.8 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

IDDetector mode
1INTEGRATING
2

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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-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0129234885
f_angle_d0.8529344651
f_chiral_restr0.052842873
f_plane_restr0.005422332
f_dihedral_angle_d15.4273129273

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