- PDB-3jah: Structure of a mammalian ribosomal termination complex with ABCE1... -
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Basic information
Entry
Database: PDB / ID: 3jah
Title
Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon
Components
(uL14) x 2
18S ribosomal RNA
28S ribosomal RNA
5.8S ribosomal RNA
5S ribosomal RNA
ABCE1
RACK1Receptor for activated C kinase 1
eL13
eL14
eL15List of Subaru engines
eL19
eL20
eL21
eL22
eL24
eL27
eL28
eL29
eL30
eL31
eL32CD59
eL33
eL34
eL36
eL37
eL38
eL39
eL40
eL41
eL42
eL43
eL6
eL8
eRF1Eukaryotic translation termination factor 1
eS1
eS10
eS12
eS17
eS19
eS21
eS24
eS25
eS26
eS27
eS28
eS30
eS31
eS4
eS6
eS7
eS8
mRNAMessenger RNA
peptide
tRNA(Lys)
tRNA(Val)
uL10
uL11
uL13
uL15
uL16
uL18
uL2
uL22
uL23
uL24
uL29
uL3
uL30
uL4
uL5
uL6
uS10
uS11
uS12
uS13
uS14
uS15
uS17
uS19
uS2
uS3
uS4
uS5
uS7
uS8
uS9
Keywords
RIBOSOME / termination / eRF1 / ABCE1
Function / homology
Function and homology information
translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / ribosomal subunit / protein methylation / mammalian oogenesis stage / activation-induced cell death of T cells ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / ribosomal subunit / protein methylation / mammalian oogenesis stage / activation-induced cell death of T cells / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / G1 to G0 transition / T cell proliferation involved in immune response / Protein hydroxylation / erythrocyte development / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / TOR signaling / ribosomal small subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / cellular response to actinomycin D / translational termination / 90S preribosome / rough endoplasmic reticulum / gastrulation / cytosolic ribosome / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / rescue of stalled ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / positive regulation of apoptotic signaling pathway / small-subunit processome / placenta development / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / spindle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome biogenesis / ribosome binding / glucose homeostasis / regulation of translation / T cell differentiation in thymus / cell body / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / mitochondrial inner membrane / tRNA binding / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of apoptotic process / positive regulation of protein phosphorylation / cell cycle / cell division / DNA repair / mRNA binding / centrosome / apoptotic process Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / 4Fe-4S binding domain / Ribosomal protein L6, N-terminal / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / TRASH domain / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L29e protein family / : / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / : / Ribosomal protein L24e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e / 40S ribosomal protein S4 C-terminus / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / RS4NT (NUC023) domain / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 60S ribosomal protein L6E / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal family S4e / Ribosomal protein S7e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L6e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein L14 / Ribosomal protein S19A/S15e / Ribosomal protein L24e signature. / Ribosomal protein S8e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L6e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Eukaryotic Ribosomal Protein L27, KOW domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL23 ...ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / ATP binding cassette subfamily E member 1 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS7 / 60S ribosomal protein L6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL3 / TRASH domain-containing protein / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL34 / Eukaryotic peptide chain release factor subunit 1 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Homo sapiens (human) Oryctolagus cuniculus (rabbit)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
Journal: Nature / Year: 2015 Title: Structural basis for stop codon recognition in eukaryotes. Authors: Alan Brown / Sichen Shao / Jason Murray / Ramanujan S Hegde / V Ramakrishnan / Abstract: Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal ...Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
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Sample preparation
Component
ID
Name
Type
Parent-ID
Synonym
1
80S ribosome-nascent chain complex containing the UAG stop codon bound to eRF1(AAQ) and ABCE1
RIBOSOME
0
2
80SribosomeEukaryotic ribosome
RIBOSOME
1
3
eukaryoticreleasefactor1, G183A, G184Amutant
1
eRF1(AAQ)
4
ATPbindingcassetteE1
1
ABCE1, Rli1
5
messengerRNA
1
6
invitrotranslatedsubstrate
1
7
tRNATransfer RNA
1
Buffer solution
Name: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT pH: 7.4 Details: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT
Specimen
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support
Details: Quantifoil R2/2 400 mesh Cu grid with thin continuous carbon support, glow discharged
Vitrification
Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % Details: After 30 second wait time, blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). Method: After 30 second wait time, blot for 3 seconds before plunging
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Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS / Date: Feb 25, 2015 / Details: Automated data acquisition using EPU (FEI)
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm
Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scans
Num. digital images: 1601
Radiation wavelength
Relative weight: 1
-
Processing
EM software
ID
Name
Version
Category
1
CTFFIND
3
CTFcorrection
2
Coot
modelfitting
3
UCSF Chimera
modelfitting
4
RELION
3Dreconstruction
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20515 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT
Atomic model building
ID
Protocol
Space
Details
1
FLEXIBLEFIT
RECIPROCAL
REFINEMENT PROTOCOL--flexible
2
FLEXIBLEFIT
RECIPROCAL
REFINEMENT PROTOCOL--flexible DETAILS--Sequence was modified in Coot to agree with rabbit sequence.
3
FLEXIBLEFIT
RECIPROCAL
REFINEMENT PROTOCOL--flexible DETAILS--Sequence was modified in Coot to agree with the most prevalent tRNA sequence for each particular codon.
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