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- PDB-5u4i: Structural Basis of Co-translational Quality Control by ArfA and ... -

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Basic information

Entry
Database: PDB / ID: 5u4i
TitleStructural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Alternative ribosome-rescue factor A
  • P-site or E-site fMet-tRNA(fMet)
  • Peptide chain release factor 2
  • mRNA
KeywordsRIBOSOME / ArfA / RF2 / nonstop translation
Function / homology
Function and homology information


translation release factor activity, codon specific / stringent response / ribosomal large subunit binding / 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 / stringent response / ribosomal large subunit binding / 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 / translational termination / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / rescue of stalled ribosome / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / viral translational frameshifting / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain ...Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / 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 L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / : / Ribosomal protein L11 signature. / 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 protein L11, N-terminal / Ribosomal L25p family / Ribosomal protein L11, N-terminal domain / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / 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 L9/RNase H1, N-terminal / 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 S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Peptide chain release factor RF2 / Large ribosomal subunit protein uL11 / 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 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 / Alternative ribosome-rescue factor A / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120552 United States
CitationJournal: Nature / Year: 2017
Title: Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.
Authors: Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin /
Abstract: Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs ...Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.
History
DepositionDec 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / em_software / Item: _em_sample_support.grid_type / _em_software.name
Revision 1.5Oct 3, 2018Group: Data collection / Other / Refinement description
Category: cell / refine ...cell / refine / refine_ls_restr / refine_ls_shell
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _refine.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.6Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
0: 50S ribosomal protein L30
1: 50S ribosomal protein L32
2: 50S ribosomal protein L33
3: 50S ribosomal protein L34
4: 50S ribosomal protein L35
5: 50S ribosomal protein L36
a: 16S rRNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: Peptide chain release factor 2
w: Alternative ribosome-rescue factor A
x: P-site or E-site fMet-tRNA(fMet)
y: P-site or E-site fMet-tRNA(fMet)
z: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,249,304182
Polymers2,246,22557
Non-polymers3,079125
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area325460 Å2
ΔGint-3695 kcal/mol
Surface area762030 Å2

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Components

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RNA chain , 5 types, 6 molecules ABaxyz

#1: RNA chain 23S rRNA


Mass: 941761.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 42756
#2: RNA chain 5S rRNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1036415628
#32: RNA chain 16S rRNA


Mass: 497044.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 817573384
#55: RNA chain P-site or E-site fMet-tRNA(fMet)


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: fMet tRNA was in vitro transcribed / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1062469497
#56: RNA chain mRNA


Mass: 5922.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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50S ribosomal protein ... , 29 types, 29 molecules CDEFGHJKLMNOPQRSTUVWXYZ012345

#3: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplB b3317 JW3279 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60422
#4: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplC b3320 JW3282 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60438
#5: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplD eryA b3319 JW3281 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60723
#6: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplE b3308 JW3270 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P62399
#7: Protein 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplF b3305 JW3267 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG55
#8: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplI b4203 JW4161 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R1
#9: Protein 50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplK relC b3983 JW3946 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7J7
#10: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplM b3231 JW3200 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AA10
#11: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplN b3310 JW3272 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY3
#12: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplO b3301 JW3263 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02413
#13: Protein 50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplP b3313 JW3275 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY7
#14: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplQ b3294 JW3256 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG44
#15: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplR b3304 JW3266 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0C018
#16: Protein 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplS b2606 JW2587 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7K6
#17: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplT pdzA b1716 JW1706 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L3
#18: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplU b3186 JW3153 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG48
#19: Protein 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplV eryB b3315 JW3277 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P61175
#20: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplW b3318 JW3280 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ0
#21: Protein 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplX b3309 JW3271 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60624
#22: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rplY b2185 JW2173 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P68919
#23: Protein 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmA b3185 JW3152 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L8
#24: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmB b3637 JW3612 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M2
#25: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmC b3312 JW3274 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M6
#26: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmD b3302 JW3264 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG51
#27: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmF b1089 JW1075 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7N4
#28: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmG b3636 JW3611 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7N9
#29: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmH rimA ssaF b3703 JW3680 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7P5
#30: Protein 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmI b1717 JW1707 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7Q1
#31: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpmJ b3299 JW3261 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7Q6

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30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#33: Protein 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsB b0169 JW0164 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V0
#34: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsC b3314 JW3276 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V3
#35: Protein 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsD ramA b3296 JW3258 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V8
#36: Protein 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsE spc b3303 JW3265 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W1
#37: Protein 30S ribosomal protein S6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsF b4200 JW4158 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358
#38: Protein 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsG b3341 JW3303 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02359
#39: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsH b3306 JW3268 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W7
#40: Protein 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsI b3230 JW3199 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7X3
#41: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsJ nusE b3321 JW3283 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R5
#42: Protein 30S ribosomal protein S11


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsK b3297 JW3259 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R9
#43: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsL strA b3342 JW3304 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S3
#44: Protein 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsM b3298 JW3260 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S9
#45: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsN b3307 JW3269 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG59
#46: Protein 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsO secC b3165 JW3134 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADZ4
#47: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsP b2609 JW2590 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T3
#48: Protein 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsQ neaA b3311 JW3273 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG63
#49: Protein 30S ribosomal protein S18


Mass: 9063.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsR b4202 JW4160 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T7
#50: Protein 30S ribosomal protein S19


Mass: 9349.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsS b3316 JW3278 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U3
#51: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsT b0023 JW0022 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U7
#52: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsU b3065 JW3037 / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P68679

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Protein , 2 types, 2 molecules vw

#53: Protein Peptide chain release factor 2 / RF-2


Mass: 43313.871 Da / Num. of mol.: 1 / Mutation: Q252MEQ
Source method: isolated from a genetically manipulated source
Details: Gene Name(s): prfB ECK2886 JW5847 supK
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: prfB, supK, b2891, JW5847 / Production host: Escherichia coli (E. coli) / References: UniProt: P07012
#54: Protein Alternative ribosome-rescue factor A


Mass: 6513.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: arfA, yhdL, b4550, JW3253 / Production host: Escherichia coli (E. coli) / References: UniProt: P36675

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Non-polymers , 2 types, 125 molecules

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


Mass: 24.305 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Non-stop ribosomal complex with ArfA and RF2COMPLEX#1-#560MULTIPLE SOURCES
230S subunitCOMPLEX#32-#521MULTIPLE SOURCES
350S subunitCOMPLEX#1-#311MULTIPLE SOURCES
4Alternative ribosome-rescue factor AORGANELLE OR CELLULAR COMPONENT#541RECOMBINANT
5Peptide chain release factor 2ORGANELLE OR CELLULAR COMPONENT#531RECOMBINANT
6P-site or E-site fMet-tRNA(fMet)ORGANELLE OR CELLULAR COMPONENT#551MULTIPLE SOURCESfMet tRNA was in vitro transcribed
7mRNAORGANELLE OR CELLULAR COMPONENT#561MULTIPLE SOURCES
823S rRNAORGANELLE OR CELLULAR COMPONENT#13NATURAL
950S ribosomal protein L2ORGANELLE OR CELLULAR COMPONENT#33NATURAL
1016S rRNAORGANELLE OR CELLULAR COMPONENT#322NATURAL
1130S ribosomal protein S2COMPLEX#332MULTIPLE SOURCES
1230S ribosomal protein S3ORGANELLE OR CELLULAR COMPONENT#342NATURAL
1330S ribosomal protein S4ORGANELLE OR CELLULAR COMPONENT#352NATURAL
1430S ribosomal protein S5ORGANELLE OR CELLULAR COMPONENT#362NATURAL
1530S ribosomal protein S6ORGANELLE OR CELLULAR COMPONENT#372NATURAL
1630S ribosomal protein S7ORGANELLE OR CELLULAR COMPONENT#382NATURAL
1730S ribosomal protein S8ORGANELLE OR CELLULAR COMPONENT#392NATURAL
1830S ribosomal protein S9ORGANELLE OR CELLULAR COMPONENT#402NATURAL
1930S ribosomal protein S10ORGANELLE OR CELLULAR COMPONENT#412NATURAL
2030S ribosomal protein S11ORGANELLE OR CELLULAR COMPONENT#422NATURAL
2130S ribosomal protein S12ORGANELLE OR CELLULAR COMPONENT#432NATURAL
2230S ribosomal protein S13ORGANELLE OR CELLULAR COMPONENT#442NATURAL
2330S ribosomal protein S14ORGANELLE OR CELLULAR COMPONENT#452NATURAL
2430S ribosomal protein S15ORGANELLE OR CELLULAR COMPONENT#462NATURAL
2530S ribosomal protein S16ORGANELLE OR CELLULAR COMPONENT#472NATURAL
2630S ribosomal protein S17ORGANELLE OR CELLULAR COMPONENT#482NATURAL
2730S ribosomal protein S18ORGANELLE OR CELLULAR COMPONENT#492NATURAL
2830S ribosomal protein S19ORGANELLE OR CELLULAR COMPONENT#502NATURAL
2930S ribosomal protein S20ORGANELLE OR CELLULAR COMPONENT#512NATURAL
3030S ribosomal protein S21ORGANELLE OR CELLULAR COMPONENT#522NATURAL
3150S ribosomal protein L3ORGANELLE OR CELLULAR COMPONENT#43NATURAL
3250S ribosomal protein L4ORGANELLE OR CELLULAR COMPONENT#53NATURAL
3350S ribosomal protein L5ORGANELLE OR CELLULAR COMPONENT#63NATURAL
3450S ribosomal protein L6ORGANELLE OR CELLULAR COMPONENT#73NATURAL
3550S ribosomal protein L9ORGANELLE OR CELLULAR COMPONENT#83NATURAL
3650S ribosomal protein L11ORGANELLE OR CELLULAR COMPONENT#93NATURAL
3750S ribosomal protein L13ORGANELLE OR CELLULAR COMPONENT#103NATURAL
3850S ribosomal protein L14ORGANELLE OR CELLULAR COMPONENT#113NATURAL
3950S ribosomal protein L15ORGANELLE OR CELLULAR COMPONENT#123NATURAL
4050S ribosomal protein L16ORGANELLE OR CELLULAR COMPONENT#133NATURAL
4150S ribosomal protein L17ORGANELLE OR CELLULAR COMPONENT#143NATURAL
4250S ribosomal protein L18ORGANELLE OR CELLULAR COMPONENT#153NATURAL
4350S ribosomal protein L19ORGANELLE OR CELLULAR COMPONENT#163NATURAL
4450S ribosomal protein L20ORGANELLE OR CELLULAR COMPONENT3NATURAL
4550S ribosomal protein L21ORGANELLE OR CELLULAR COMPONENT#183NATURAL
4650S ribosomal protein L22ORGANELLE OR CELLULAR COMPONENT#193NATURAL
4750S ribosomal protein L23ORGANELLE OR CELLULAR COMPONENT#203NATURAL
4850S ribosomal protein L24ORGANELLE OR CELLULAR COMPONENT#213NATURAL
4950S ribosomal protein L25COMPLEX#223NATURAL
5050S ribosomal protein L27ORGANELLE OR CELLULAR COMPONENT#233NATURAL
5150S ribosomal protein L28ORGANELLE OR CELLULAR COMPONENT#243NATURAL
5250S ribosomal protein L29ORGANELLE OR CELLULAR COMPONENT#253NATURAL
5350S ribosomal protein L30ORGANELLE OR CELLULAR COMPONENT#263NATURAL
5450S ribosomal protein L32ORGANELLE OR CELLULAR COMPONENT#273NATURAL
5550S ribosomal protein L33ORGANELLE OR CELLULAR COMPONENT#283NATURAL
5650S ribosomal protein L34ORGANELLE OR CELLULAR COMPONENT#293NATURAL
5750S ribosomal protein L35ORGANELLE OR CELLULAR COMPONENT#303NATURAL
5850S ribosomal protein L36ORGANELLE OR CELLULAR COMPONENT#313NATURAL
595S rRNAORGANELLE OR CELLULAR COMPONENT#23NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11
12
13
246.35 kDa/nmNO
3540.13 kDa/nmNO
16
17
18
19
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
24Escherichia coli (E. coli)562
35Escherichia coli (E. coli)562
28Escherichia coli (E. coli)562
39Escherichia coli (E. coli)562
410Escherichia coli (E. coli)562
511Escherichia coli (E. coli)562
612Escherichia coli (E. coli)562
713Escherichia coli (E. coli)562
814Escherichia coli (E. coli)562
915Escherichia coli (E. coli)562
1016Escherichia coli (E. coli)562
1117Escherichia coli (E. coli)562
1218Escherichia coli (E. coli)562
1319Escherichia coli (E. coli)562
1420Escherichia coli (E. coli)562
1521Escherichia coli (E. coli)562
1622Escherichia coli (E. coli)562
1723Escherichia coli (E. coli)562
1824Escherichia coli (E. coli)562
1925Escherichia coli (E. coli)562
2026Escherichia coli (E. coli)562
2127Escherichia coli (E. coli)562
2228Escherichia coli (E. coli)562
2329Escherichia coli (E. coli)562
2430Escherichia coli (E. coli)562
2531Escherichia coli (E. coli)562
2632Escherichia coli (E. coli)562
2733Escherichia coli (E. coli)562
2834Escherichia coli (E. coli)562
2935Escherichia coli (E. coli)562
3036Escherichia coli (E. coli)562
3137Escherichia coli (E. coli)562
3238Escherichia coli (E. coli)562
3339Escherichia coli (E. coli)562
3440Escherichia coli (E. coli)562
3541Escherichia coli (E. coli)562
3642Escherichia coli (E. coli)562
3743Escherichia coli (E. coli)562
3844Escherichia coli (E. coli)562
3945Escherichia coli (E. coli)562
4046Escherichia coli (E. coli)562
4147Escherichia coli (E. coli)562
4248Escherichia coli (E. coli)562
4349Escherichia coli (E. coli)562
4450Escherichia coli (E. coli)562
4551Escherichia coli (E. coli)562
4652Escherichia coli (E. coli)562
4753Escherichia coli (E. coli)562
4854Escherichia coli (E. coli)562
4955Escherichia coli (E. coli)562
5056Escherichia coli (E. coli)562
5157Escherichia coli (E. coli)562
5258Escherichia coli (E. coli)562
5359Escherichia coli (E. coli)562
11Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
24Escherichia coli (E. coli)562BL21pET28
35Escherichia coli (E. coli)562BL21pETNKI-his3C-LIC-Kan
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidC8H18N2O4S1
215 mMmagnesium acetateMg(CH3COO)21
3150 mMpotassium acetateCH3CO2K1
44 mM2-mercapthoethanolHOCH2CH2SH1
52 mMspermidineC7H19N31
60.05 mMsperminC10H26N41
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/0.5 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 83822 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 20 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 4-25

-
Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
12RELION23D reconstruction
13REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155440 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: Average FSC
RefinementResolution: 3.5→458.112 Å / Cor.coef. Fo:Fc: 0.768 / WRfactor Rwork: 0.384 / SU B: 29.504 / SU ML: 0.382 / ESU R: 0.257
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3838 4696443 -
all0.384 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 303.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.453 Å21.509 Å2-1.254 Å2
2--3.23 Å22.7 Å2
3----2.778 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.014165101
ELECTRON MICROSCOPYr_ext_dist_refined_d0.1060.0229707
ELECTRON MICROSCOPYr_angle_refined_deg0.9471.469242315
ELECTRON MICROSCOPYr_dihedral_angle_1_deg20.8439.79833567
ELECTRON MICROSCOPYr_dihedral_angle_2_deg43.40522.5031742
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.728157469
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.77315454
ELECTRON MICROSCOPYr_chiral_restr0.1290.21727721
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0285395
ELECTRON MICROSCOPYr_nbd_refined0.1560.2139524
ELECTRON MICROSCOPYr_nbtor_refined0.2730.2197596
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1280.26720
ELECTRON MICROSCOPYr_metal_ion_refined0.0990.270
ELECTRON MICROSCOPYr_paralell_plane_angle_deg4.1081.23447
ELECTRON MICROSCOPYr_mcbond_it4.70833.95624596
ELECTRON MICROSCOPYr_mcangle_it8.6650.91530654
ELECTRON MICROSCOPYr_scbond_it4.08829.51140505
ELECTRON MICROSCOPYr_scangle_it7.07544.245211661
ELECTRON MICROSCOPYr_lrange_it23.169816.292683576
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkNum. reflection allWRfactor Rwork
3.5-3.5910.5893475943475940.589
3.591-3.6890.5743391313391310.574
3.689-3.7960.5523293003293000.552
3.796-3.9130.5383200993200990.538
3.913-4.0410.513098003098000.51
4.041-4.1830.4782998222998220.478
4.183-4.3410.452895302895300.45
4.341-4.5180.4252784382784380.425
4.518-4.7190.4032671462671460.403
4.719-4.950.3882548292548290.388
4.95-5.2170.3642429492429490.364
5.217-5.5340.3572294072294070.357
5.534-5.9160.3422157752157750.342
5.916-6.390.3352007062007060.335
6.39-6.9990.3341846541846540.334
6.999-7.8250.3141670471670470.314
7.825-9.0350.3131472081472080.313
9.035-11.0650.2911242871242870.291
11.065-15.6440.29296022960220.292
15.644-458.1120.41652699526990.416

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