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- PDB-9i3l: Structure of E.coli ribosome with filamin mutant Y719E nascent ch... -

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Entry
Database: PDB / ID: 9i3l
TitleStructure of E.coli ribosome with filamin mutant Y719E nascent chain at linker length of 47 amino acids, with tRNA
Components
  • (50S ribosomal protein ...) x 3
  • (Large ribosomal subunit protein ...) x 25
  • 23S rRNA
  • 5S rRNA
  • Gelation factor
  • Peptidyl Gly-tRNA
KeywordsRIBOSOME / exit tunnel / nascent chain / stalling
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / slug development involved in sorocarp development / pseudopodium assembly / positive phototaxis / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / slug development involved in sorocarp development / pseudopodium assembly / positive phototaxis / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / mitogen-activated protein kinase binding / hyperosmotic response / lamellipodium assembly / cortical actin cytoskeleton / pseudopodium / cell leading edge / response to cAMP / phagocytosis / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / phagocytic cup / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / extracellular matrix / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / ribosome assembly / regulation of cell growth / cell motility / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / small GTPase binding / actin filament binding / cell migration / large ribosomal subunit / transferase activity / ribosome binding / actin cytoskeleton organization / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cell cortex / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / : / Ribosomal protein L25, short-form / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9 / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / 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 bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Gelation factor / 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 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMitropoulou, A. / Wlodarski, T. / Plessa, E. / Cabrita, L.D. / Christodoulou, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: The ribosome directs nascent chains through two folding-dependent pathways
Authors: Mitropoulou, A. / Wlodarski, T. / Streit, J.O. / Plessa, E. / Chan, S.H. / Cabrita, L.D. / Christodoulou, J.
History
DepositionJan 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
2: Large ribosomal subunit protein uL30
3: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL33
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: 50S ribosomal protein L36
a: 5S rRNA
b: 23S rRNA
c: Large ribosomal subunit protein uL2
d: 50S ribosomal protein L3
e: Large ribosomal subunit protein uL4
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL9
j: Large ribosomal subunit protein uL13
k: Large ribosomal subunit protein uL14
l: Large ribosomal subunit protein uL15
m: 50S ribosomal protein L16
n: Large ribosomal subunit protein bL17
o: Large ribosomal subunit protein uL18
p: Large ribosomal subunit protein bL19
q: Large ribosomal subunit protein bL20
r: Large ribosomal subunit protein bL21
s: Large ribosomal subunit protein uL22
t: Large ribosomal subunit protein uL23
u: Large ribosomal subunit protein uL24
w: Large ribosomal subunit protein bL25
y: Large ribosomal subunit protein bL27
z: Gelation factor
Z: Peptidyl Gly-tRNA


Theoretical massNumber of molelcules
Total (without water)1,385,49632
Polymers1,385,49632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 25 types, 25 molecules 0123467cefghjklnopqrstuwy

#1: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#2: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#3: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#4: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#5: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#6: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#7: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#11: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#13: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#14: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#15: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#16: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#17: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#18: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#19: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#21: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#22: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#23: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#24: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#25: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#26: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#27: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#28: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#29: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#30: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8

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50S ribosomal protein ... , 3 types, 3 molecules 8dm

#8: Protein/peptide 50S ribosomal protein L36


Mass: 5720.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2X1PTA3
#12: Protein 50S ribosomal protein L3 / ribosomal protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#20: Protein 50S ribosomal protein L16 / ribosomal protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7

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RNA chain , 3 types, 3 molecules abZ

#9: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP035706.1
#10: RNA chain 23S rRNA


Mass: 941620.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 2065591978
#32: RNA chain Peptidyl Gly-tRNA


Mass: 24478.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1851733809

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Protein , 1 types, 1 molecules z

#31: Protein Gelation factor / Actin-binding protein 120 / ABP-120


Mass: 17003.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: abpC, DDB_G0269100 / Production host: Escherichia coli (E. coli) / References: UniProt: P13466

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Ribosomal nascent chain of Y719E FLN5 mutant with linker length 47
Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 37.272 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Category: classification
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143483 / Symmetry type: POINT

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