translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. 類似検索 - ドメイン・相同性
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Peptide chain release factor 2 / Uncharacterized protein YqkK / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 類似検索 - 構成要素
ジャーナル: Nat Commun / 年: 2019 タイトル: Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. 著者: Naomi Shimokawa-Chiba / Claudia Müller / Keigo Fujiwara / Bertrand Beckert / Koreaki Ito / Daniel N Wilson / Shinobu Chiba / 要旨: Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some ...Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems.
ダウンロード / ファイル: emd_10353.map.gz / 形式: CCP4 / 大きさ: 190.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
ボクセルのサイズ
X=Y=Z: 1.065 Å
密度
表面レベル
登録者による: 0.0387 / ムービー #1: 0.0387
最小 - 最大
-0.0672588 - 0.18675235
平均 (標準偏差)
0.0014536924 (±0.008728551)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
368
368
368
Spacing
368
368
368
セル
A=B=C: 391.92 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.065
1.065
1.065
M x/y/z
368
368
368
origin x/y/z
0.000
0.000
0.000
length x/y/z
391.920
391.920
391.920
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
111
-94
150
NX/NY/NZ
111
123
111
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
368
368
368
D min/max/mean
-0.067
0.187
0.001
-
添付データ
-
試料の構成要素
+
全体 : E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
全体
名称: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2-Q251P
要素
複合体: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2-Q251P
複合体: Escherichia coli ribosome with P-site tRNA-Pro(CGG, carrying the nascent chain
タンパク質・ペプチド: 50S ribosomal protein L32
タンパク質・ペプチド: 50S ribosomal protein L33
タンパク質・ペプチド: 50S ribosomal protein L34
タンパク質・ペプチド: 50S ribosomal protein L35
タンパク質・ペプチド: 50S ribosomal protein L36
タンパク質・ペプチド: 50S ribosomal protein L31
RNA: 23S ribosomal RNA
RNA: 5S ribosomal RNA
タンパク質・ペプチド: 50S ribosomal protein L2
タンパク質・ペプチド: 50S ribosomal protein L3
タンパク質・ペプチド: 50S ribosomal protein L4
タンパク質・ペプチド: 50S ribosomal protein L5
タンパク質・ペプチド: 50S ribosomal protein L6
タンパク質・ペプチド: 50S ribosomal protein L9
タンパク質・ペプチド: 50S ribosomal protein L13
タンパク質・ペプチド: 50S ribosomal protein L14
タンパク質・ペプチド: 50S ribosomal protein L15
タンパク質・ペプチド: 50S ribosomal protein L16
タンパク質・ペプチド: 50S ribosomal protein L17
タンパク質・ペプチド: 50S ribosomal protein L18
タンパク質・ペプチド: 50S ribosomal protein L19
タンパク質・ペプチド: 50S ribosomal protein L20
タンパク質・ペプチド: 50S ribosomal protein L21
タンパク質・ペプチド: 50S ribosomal protein L22
タンパク質・ペプチド: 50S ribosomal protein L23
タンパク質・ペプチド: 50S ribosomal protein L24
タンパク質・ペプチド: 50S ribosomal protein L25
タンパク質・ペプチド: 50S ribosomal protein L27
タンパク質・ペプチド: 50S ribosomal protein L28
タンパク質・ペプチド: 50S ribosomal protein L29
タンパク質・ペプチド: 50S ribosomal protein L30
RNA: 16S ribosomal RNA
タンパク質・ペプチド: 30S ribosomal protein S2
タンパク質・ペプチド: 30S ribosomal protein S3
タンパク質・ペプチド: 30S ribosomal protein S4
タンパク質・ペプチド: 30S ribosomal protein S5
タンパク質・ペプチド: 30S ribosomal protein S6
タンパク質・ペプチド: 30S ribosomal protein S7
タンパク質・ペプチド: 30S ribosomal protein S8
タンパク質・ペプチド: 30S ribosomal protein S9
タンパク質・ペプチド: 30S ribosomal protein S10
タンパク質・ペプチド: 30S ribosomal protein S11
タンパク質・ペプチド: 30S ribosomal protein S12
タンパク質・ペプチド: 30S ribosomal protein S13
タンパク質・ペプチド: 30S ribosomal protein S14
タンパク質・ペプチド: 30S ribosomal protein S15
タンパク質・ペプチド: 30S ribosomal protein S16
タンパク質・ペプチド: 30S ribosomal protein S17
タンパク質・ペプチド: 30S ribosomal protein S18
タンパク質・ペプチド: 30S ribosomal protein S19
タンパク質・ペプチド: 30S ribosomal protein S20
タンパク質・ペプチド: 30S ribosomal protein S21
RNA: mRNA
RNA: P-site tRNA-Pro(CGG)
複合体: Bacillus subtilis ribosome rescue factor (BrfA; former YqkK) and peptide chain release factor 2 (RF2)
タンパク質・ペプチド: Uncharacterized protein YqkK
タンパク質・ペプチド: Peptide chain release factor 2
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超分子 #1: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
超分子
名称: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2-Q251P タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#56 詳細: E. coli 70S stalled on truncated mRNA in complex with Bacillus ribosome rescue factor A (BrfA) and a hydrolysis deminished mutant of Bacillus peptide chain release factor 2 (RF2-Q251P)
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超分子 #2: Escherichia coli ribosome with P-site tRNA-Pro(CGG, carrying the ...
MAKSQAKKKR GHRLRNGGRD VLLSRGSTPS FSTHGRMTKS KKEILNKRKH KNPYDHTAVD DKDFFVPQKA A
UniProtKB: Uncharacterized protein YqkK
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分子 #56: Peptide chain release factor 2
分子
名称: Peptide chain release factor 2 / タイプ: protein_or_peptide / ID: 56 詳細: -Q251P mutation (hydrolysis defective release factor) -low resolution regions were only the backbone was traced were kept as ALA コピー数: 1 / 光学異性体: LEVO