- PDB-3jag: Structure of a mammalian ribosomal termination complex with ABCE1... -
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Basic information
Entry
Database: PDB / ID: 3jag
Title
Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codon
Components
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
eL18
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
uL14
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 / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / ribosomal subunit / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / ribosomal subunit / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / translational termination / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / : / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / ribosome binding / ribosome biogenesis / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / cytosol / cytoplasm 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 / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal L28e protein family / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / TRASH domain / Ribosomal protein L29e / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S12e signature. / Ribosomal protein S27a / Ribosomal protein L24e, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e / 40S Ribosomal protein S10 / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein L44 / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / RS4NT (NUC023) domain / 60S ribosomal protein L6E / Ribosomal protein S27 / Ribosomal protein S17e signature. / Ribosomal protein L44e signature. / Ribosomal family S4e / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / Ribosomal protein L6e / Ribosomal protein S6e / Ribosomal L37ae protein family / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein L35Ae / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L31e / Ribosomal protein L6, conserved site-2 / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein L35Ae signature. / Ribosomal L39 protein / Ribosomal protein S28e signature. / Ribosomal protein L37e / Ribosomal protein L24e / Ribosomal L15 / Ribosomal protein L31e signature. / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14 / Ribosomal protein L6 signature 2. / Ribosomal protein L14, KOW motif / Ribosomal protein L1e signature. / Ribosomal protein S8e Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L41 / 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) / 60S ribosomal protein L41 / 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 / Ribosomal protein S14 / 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 / Plectin/eS10 N-terminal domain-containing protein / 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 / Ribosomal protein L32 / 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: 3.65 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 UAA 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
Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scans
Num. digital images: 2672
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Processing
EM software
ID
Name
Version
Category
1
CTFFIND
3
CTFcorrection
2
Coot
modelfitting
3
UCSF Chimera
modelfitting
4
RELION
3Dreconstruction
5
EPU
imageacquisition
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49979 / 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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