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- PDB-8uu8: Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiv... -

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Basic information

Entry
Database: PDB / ID: 8uu8
TitleCryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-C)
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 19
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • F-Stop mRNA
  • GTPase HflX
  • pe/E Hybrid State Phenylalanine tRNA
KeywordsRIBOSOME / recycling / HflXr / time-resolved
Function / homology
Function and homology information


large ribosomal subunit / ribosome binding / transferase activity / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / ribosome binding / transferase activity / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 type B / Type-1 KH domain profile. ...GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 type B / Type-1 KH domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / : / 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 S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / 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 S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL31B ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / : / : / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS6 / GTPase HflX
Similarity search - Component
Biological speciesListeria innocua (bacteria)
Escherichia coli (E. coli)
Listeria monocytogenes EGD-e (bacteria)
Escherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSeely, S.M. / Basu, R.S. / Gagnon, M.G.
Funding support United States, 4items
OrganizationGrant numberCountry
Other governmentUniversity of Texas Medical Branch Startup Funds
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136936 United States
Welch FoundationH-2032-20230405 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008280 United States
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Mechanistic insights into the alternative ribosome recycling by HflXr.
Authors: Savannah M Seely / Ritwika S Basu / Matthieu G Gagnon /
Abstract: During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue ...During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
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Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: 16S Ribosomal RNA
b: Small ribosomal subunit protein uS2
c: Small ribosomal subunit protein uS3
d: Small ribosomal subunit protein uS4
e: Small ribosomal subunit protein uS5
f: Small ribosomal subunit protein bS6
g: Small ribosomal subunit protein uS7
h: Small ribosomal subunit protein uS8
i: Small ribosomal subunit protein uS9
j: Small ribosomal subunit protein uS10
k: Small ribosomal subunit protein uS11
l: Small ribosomal subunit protein uS12
m: Small ribosomal subunit protein uS13
n: Small ribosomal subunit protein uS14
o: Small ribosomal subunit protein uS15
p: Small ribosomal subunit protein bS16
q: Small ribosomal subunit protein uS17
r: Small ribosomal subunit protein bS18
s: Small ribosomal subunit protein uS19
t: Small ribosomal subunit protein bS20
x: pe/E Hybrid State Phenylalanine tRNA
w: F-Stop mRNA
v: GTPase HflX
A: 23S Ribosomal RNA
B: 5S Ribosomal RNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
I: Large ribosomal subunit protein uL10
H: Large ribosomal subunit protein uL11
L: Large ribosomal subunit protein uL13
M: Large ribosomal subunit protein uL14
N: Large ribosomal subunit protein uL15
O: Large ribosomal subunit protein uL16
P: Large ribosomal subunit protein bL17
Q: Large ribosomal subunit protein uL18
R: Large ribosomal subunit protein bL19
S: Large ribosomal subunit protein bL20
T: Large ribosomal subunit protein bL21
U: Large ribosomal subunit protein uL22
V: Large ribosomal subunit protein uL23
W: Large ribosomal subunit protein uL24
Y: Large ribosomal subunit protein bL27
Z: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
2: Large ribosomal subunit protein uL30
3: Large ribosomal subunit protein bL31B
4: Large ribosomal subunit protein bL32
5: Large ribosomal subunit protein bL33
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: Large ribosomal subunit protein bL36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,235,459482
Polymers2,224,39554
Non-polymers11,064428
Water6,557364
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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RNA chain , 5 types, 5 molecules axwAB

#1: RNA chain 16S Ribosomal RNA


Mass: 501949.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 2027972510
#21: RNA chain pe/E Hybrid State Phenylalanine tRNA


Mass: 24644.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1850831943
#22: RNA chain F-Stop mRNA


Mass: 6792.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic 21-nt F-Stop mRNA / Source: (synth.) Escherichia phage T4 (virus)
#24: RNA chain 23S Ribosomal RNA


Mass: 951061.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 2288068686
#25: RNA chain 5S Ribosomal RNA


Mass: 37304.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 1774324476

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Small ribosomal subunit protein ... , 19 types, 19 molecules bcdefghijklmnopqrst

#2: Protein Small ribosomal subunit protein uS2


Mass: 28359.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A6B0JGP5
#3: Protein Small ribosomal subunit protein uS3


Mass: 24587.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSU9
#4: Protein Small ribosomal subunit protein uS4


Mass: 22716.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A6B0JGH8
#5: Protein Small ribosomal subunit protein uS5


Mass: 17516.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSJ3
#6: Protein Small ribosomal subunit protein bS6


Mass: 11512.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A7X0WKH5
#7: Protein Small ribosomal subunit protein uS7


Mass: 17848.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JPE1
#8: Protein Small ribosomal subunit protein uS8


Mass: 14667.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A6U3
#9: Protein Small ribosomal subunit protein uS9


Mass: 14473.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ADS9
#10: Protein Small ribosomal subunit protein uS10


Mass: 11703.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A730
#11: Protein Small ribosomal subunit protein uS11


Mass: 13812.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AP31
#12: Protein Small ribosomal subunit protein uS12


Mass: 15216.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JM56
#13: Protein Small ribosomal subunit protein uS13


Mass: 13738.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ARJ0
#14: Protein Small ribosomal subunit protein uS14


Mass: 7164.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AGZ1
#15: Protein Small ribosomal subunit protein uS15


Mass: 10656.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JLK4
#16: Protein Small ribosomal subunit protein bS16


Mass: 10404.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A6B0JQE1
#17: Protein Small ribosomal subunit protein uS17


Mass: 10057.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ADR4
#18: Protein Small ribosomal subunit protein bS18


Mass: 9119.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JK14
#19: Protein Small ribosomal subunit protein uS19


Mass: 10498.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSH5
#20: Protein Small ribosomal subunit protein bS20


Mass: 9189.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JML5

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Protein , 1 types, 1 molecules v

#23: Protein GTPase HflX


Mass: 47610.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / Strain: ATCCBAA-679 / References: UniProt: Q8Y8Y0

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Large ribosomal subunit protein ... , 29 types, 29 molecules CDEFGIHLMNOPQRSTUVWYZ12345678

#26: Protein Large ribosomal subunit protein uL2


Mass: 30568.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A742
#27: Protein Large ribosomal subunit protein uL3


Mass: 22880.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ADD0
#28: Protein Large ribosomal subunit protein uL4


Mass: 22640.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSH7
#29: Protein Large ribosomal subunit protein uL5


Mass: 20023.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AWX6
#30: Protein Large ribosomal subunit protein uL6


Mass: 19433.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ALU0
#31: Protein Large ribosomal subunit protein uL10


Mass: 17715.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A6T9
#32: Protein Large ribosomal subunit protein uL11


Mass: 14878.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JML6
#33: Protein Large ribosomal subunit protein uL13


Mass: 16228.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AGN0
#34: Protein Large ribosomal subunit protein uL14


Mass: 13248.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AP82
#35: Protein Large ribosomal subunit protein uL15


Mass: 15827.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A6S7
#36: Protein Large ribosomal subunit protein uL16


Mass: 16171.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSU8
#37: Protein Large ribosomal subunit protein bL17


Mass: 15237.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSW3
#38: Protein Large ribosomal subunit protein uL18


Mass: 13107.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AR65
#39: Protein Large ribosomal subunit protein bL19


Mass: 13089.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A6B0JQF2
#40: Protein Large ribosomal subunit protein bL20


Mass: 13719.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JH71
#41: Protein Large ribosomal subunit protein bL21


Mass: 11220.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AD18
#42: Protein Large ribosomal subunit protein uL22


Mass: 12895.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ANW2
#43: Protein Large ribosomal subunit protein uL23


Mass: 10949.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4MTC5
#44: Protein Large ribosomal subunit protein uL24


Mass: 11219.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AD05
#45: Protein Large ribosomal subunit protein bL27


Mass: 10571.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JMC7
#46: Protein Large ribosomal subunit protein bL28


Mass: 7010.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JJV9
#47: Protein Large ribosomal subunit protein uL29


Mass: 7414.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AGL9
#48: Protein Large ribosomal subunit protein uL30


Mass: 6504.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSJ1
#49: Protein Large ribosomal subunit protein bL31B


Mass: 9274.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4MT39
#50: Protein Large ribosomal subunit protein bL32


Mass: 6534.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JNN0
#51: Protein/peptide Large ribosomal subunit protein bL33


Mass: 6021.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JRA4
#52: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5319.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JKZ6
#53: Protein Large ribosomal subunit protein bL35


Mass: 7746.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JIB9
#54: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4336.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AM58

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Non-polymers , 4 types, 792 molecules

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


Mass: 24.305 Da / Num. of mol.: 423 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#57: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: Listeria innocua 70S ribosome in complex with HflXr and pe/E-tRNA
Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Listeria innocua (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 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 magnification: 96000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10151

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
2SerialEMimage acquisition
3cryoSPARC4.1.2masking
4cryoSPARC4.1.2CTF correction
7UCSF Chimera1.14model fitting
8PHENIX1.19.2.4158model refinement
10cryoSPARC4.1.2initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12cryoSPARC4.1.2classification
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55099 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7NHN

7nhn


Accession code: 7NHN / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002153724
ELECTRON MICROSCOPYf_angle_d0.498230775
ELECTRON MICROSCOPYf_dihedral_angle_d14.37761720
ELECTRON MICROSCOPYf_chiral_restr0.03229812
ELECTRON MICROSCOPYf_plane_restr0.00412166

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