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- PDB-8qcq: B. subtilis ApdA-stalled ribosomal complex -

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Basic information

Entry
Database: PDB / ID: 8qcq
TitleB. subtilis ApdA-stalled ribosomal complex
Components
  • (30S ribosomal protein ...) x 14
  • (50S ribosomal protein ...) x 21
  • (Large ribosomal subunit protein ...) x 6
  • (Small ribosomal subunit protein ...) x 2
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • ApdA nascent chain
  • Pro-tRNA
  • mRNA
KeywordsRIBOSOME / Stalling / Nascent chain / elongation arrest / regulation
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / 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 / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...: / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S14/S29 / 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 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 / L28p-like / Ribosomal protein S15, bacterial-type / : / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34
Similarity search - Domain/homology
: / PROLINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / PROLINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesAmycolatopsis japonica (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMorici, M. / Wilson, D.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.
Authors: Martino Morici / Sara Gabrielli / Keigo Fujiwara / Helge Paternoga / Bertrand Beckert / Lars V Bock / Shinobu Chiba / Daniel N Wilson /
Abstract: Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein ...Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.
History
DepositionAug 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
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Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
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Revision 1.1Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33 1
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: Large ribosomal subunit protein bL31-A
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: Large ribosomal subunit protein uL6
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: Large ribosomal subunit protein bL20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: Large ribosomal subunit protein uL23
U: 50S ribosomal protein L24
W: Large ribosomal subunit protein bL27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: Large ribosomal subunit protein uL30
a: 16S rRNA
e: 30S ribosomal protein S5
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
o: 30S ribosomal protein S15
q: 30S ribosomal protein S17
t: 30S ribosomal protein S20
y: Pro-tRNA
w: Pro-tRNA
8: mRNA
c: Small ribosomal subunit protein uS3
g: Small ribosomal subunit protein uS7
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
s: 30S ribosomal protein S19
h: 30S ribosomal protein S8
r: 30S ribosomal protein S18
f: 30S ribosomal protein S6
7: ApdA nascent chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,105,870298
Polymers2,098,91050
Non-polymers6,960248
Water18,4111022
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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50S ribosomal protein ... , 21 types, 21 molecules 01234CDEFJKLMNOPRSUXY

#1: Protein 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#2: Protein/peptide 50S ribosomal protein L33 1


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#4: Protein 50S ribosomal protein L35


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#5: Protein/peptide 50S ribosomal protein L36 / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#9: Protein 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#10: Protein 50S ribosomal protein L3 / BL3


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#11: Protein 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#12: Protein 50S ribosomal protein L5 / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#14: Protein 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#15: Protein 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#16: Protein 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#17: Protein 50S ribosomal protein L16


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#18: Protein 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#19: Protein 50S ribosomal protein L18 / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#20: Protein 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#22: Protein 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#23: Protein 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#25: Protein 50S ribosomal protein L24 / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#27: Protein 50S ribosomal protein L28


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#28: Protein 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873

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Large ribosomal subunit protein ... , 6 types, 6 molecules 6GQTWZ

#6: Protein Large ribosomal subunit protein bL31-A


Mass: 7330.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223
#13: Protein Large ribosomal subunit protein uL6


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#21: Protein Large ribosomal subunit protein bL20


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#24: Protein Large ribosomal subunit protein uL23


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#26: Protein Large ribosomal subunit protein bL27


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#29: Protein Large ribosomal subunit protein uL30


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947

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RNA chain , 5 types, 6 molecules ABayw8

#7: RNA chain 23S rRNA


Mass: 948733.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 728882887
#8: RNA chain 5S rRNA


Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1430100595
#30: RNA chain 16S rRNA


Mass: 503369.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 225184640
#37: RNA chain Pro-tRNA


Mass: 24832.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1837880844
#38: RNA chain mRNA


Mass: 1788.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis japonica (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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30S ribosomal protein ... , 14 types, 14 molecules ekloqtijmnshrf

#31: Protein 30S ribosomal protein S5 / BS5


Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#32: Protein 30S ribosomal protein S11 / BS11


Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#33: Protein 30S ribosomal protein S12 / BS12


Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#34: Protein 30S ribosomal protein S15 / BS18


Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#35: Protein 30S ribosomal protein S17 / BS16


Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#36: Protein 30S ribosomal protein S20 / BS20


Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477
#41: Protein 30S ribosomal protein S9 / BS10


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#42: Protein 30S ribosomal protein S10 / BS13


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#43: Protein 30S ribosomal protein S13 / BS14


Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#44: Protein 30S ribosomal protein S14 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S14-1 / BS-A


Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#45: Protein 30S ribosomal protein S19 / BS19


Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#46: Protein 30S ribosomal protein S8 / BS8


Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#47: Protein 30S ribosomal protein S18 / BS21


Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#48: Protein 30S ribosomal protein S6 / BS9


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468

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Small ribosomal subunit protein ... , 2 types, 2 molecules cg

#39: Protein Small ribosomal subunit protein uS3


Mass: 23050.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#40: Protein Small ribosomal subunit protein uS7


Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469

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Protein/peptide , 1 types, 1 molecules 7

#49: Protein/peptide ApdA nascent chain


Mass: 970.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis japonica (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Non-polymers , 5 types, 1270 molecules

#50: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#51: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 199 / Source method: obtained synthetically / Formula: Mg
#52: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: K
#53: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#54: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: B. subtilis ApdA-stalled ribosomal complex / Type: RIBOSOME / Entity ID: #3-#4, #8-#43, #45-#49 / Source: RECOMBINANT
Source (natural)Organism: Amycolatopsis japonica (bacteria)
Source (recombinant)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 75.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0405 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142978 / Symmetry type: POINT
RefinementResolution: 2.3→2.3 Å / Cor.coef. Fo:Fc: 0.931 / SU B: 5.999 / SU ML: 0.129 / ESU R: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.26202 --
obs0.26202 3119422 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 83.844 Å2
Refinement stepCycle: 1 / Total: 136962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.011148315
ELECTRON MICROSCOPYr_bond_other_d0.0010.01883779
ELECTRON MICROSCOPYr_angle_refined_deg1.4161.799222326
ELECTRON MICROSCOPYr_angle_other_deg0.5581.626198257
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.94154776
ELECTRON MICROSCOPYr_dihedral_angle_2_deg7.4655.011440
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.408107548
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0590.233105
ELECTRON MICROSCOPYr_gen_planes_refined0.010.02100188
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0226180
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.0158.48119242
ELECTRON MICROSCOPYr_mcbond_other7.0158.48119242
ELECTRON MICROSCOPYr_mcangle_it11.56115.28723972
ELECTRON MICROSCOPYr_mcangle_other11.56115.28723973
ELECTRON MICROSCOPYr_scbond_it6.4438.549129073
ELECTRON MICROSCOPYr_scbond_other6.4438.549129072
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other10.40115.567198355
ELECTRON MICROSCOPYr_long_range_B_refined15.40493.75190132
ELECTRON MICROSCOPYr_long_range_B_other15.4193.86189768
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.638 231056 -
obs--100 %

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