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- PDB-8cd1: 70S-PHIKZ014 -

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Basic information

Entry
Database: PDB / ID: 8cd1
Title70S-PHIKZ014
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 27
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Large ribosomal subunit protein uL22
  • PHIKZ014
  • tRNATransfer RNA
KeywordsRIBOSOME / PHIKZ / Phage / hijacked / bacterial / Pseudomonas / PHIKZ014 / 5S rRNA
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / 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 L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / PHIKZ014 / Large ribosomal subunit protein bL28 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / PHIKZ014 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36A / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Pseudomonas phage phiKZ (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsGerovac, M. / Vogel, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Microbiol / Year: 2024
Title: Phage proteins target and co-opt host ribosomes immediately upon infection.
Authors: Milan Gerovac / Kotaro Chihara / Laura Wicke / Bettina Böttcher / Rob Lavigne / Jörg Vogel /
Abstract: Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general ...Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general understanding of phage mechanisms for immediate targeting of host transcription and translation processes is lacking. Here we introduce an integrative high-throughput approach to uncover phage-encoded proteins that target the gene expression machinery of Pseudomonas aeruginosa immediately upon infection with the jumbo phage ΦKZ. By integrating biochemical, genetic and structural analyses, we identify an abundant and conserved phage factor ΦKZ014 that targets the large ribosomal subunit by binding the 5S ribosomal RNA, and rapidly promotes replication in several clinical isolates. ΦKZ014 is among the earliest ΦKZ proteins expressed after infection and remains bound to ribosomes during the entire translation cycle. Our study provides a strategy to decipher molecular components of phage-mediated host takeover and argues that phage genomes represent an untapped discovery space for proteins that modulate the host gene expression machinery.
History
DepositionJan 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 50S ribosomal protein L32
4: 50S ribosomal protein L34
5: 50S ribosomal protein L35
6: 50S ribosomal protein L36
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
Dt: tRNA
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
Le: 50S ribosomal protein L31
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: Large ribosomal subunit protein uL22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
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: PHIKZ014
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,203,922224
Polymers2,199,76653
Non-polymers4,156171
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area279500 Å2
ΔGint-3724 kcal/mol
Surface area792210 Å2

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Components

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50S ribosomal protein ... , 27 types, 27 molecules 2456CDEFGHJKLLeMNOPQRTUVWXYZ

#1: Protein 50S ribosomal protein L32 /


Mass: 6807.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmF, PA2970 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HZN4
#2: Protein/peptide 50S ribosomal protein L34 /


Mass: 5226.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmH, PA5570 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P29436
#3: Protein 50S ribosomal protein L35 /


Mass: 7387.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / References: UniProt: Q9I0A1
#4: Protein/peptide 50S ribosomal protein L36 /


Mass: 4447.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmJ, PA4242 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF6
#7: Protein 50S ribosomal protein L2 /


Mass: 29641.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD8
#8: Protein 50S ribosomal protein L3 /


Mass: 22625.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplC, PA4263 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD5
#10: Protein 50S ribosomal protein L4 /


Mass: 21673.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplD, PA4262 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD6
#11: Protein 50S ribosomal protein L5 /


Mass: 20424.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplE, PA4251 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE7
#12: Protein 50S ribosomal protein L6 /


Mass: 19129.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplF, PA4248 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF0
#13: Protein 50S ribosomal protein L9 /


Mass: 15551.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplI, PA4932 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUN2
#14: Protein 50S ribosomal protein L13 /


Mass: 16058.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplM, PA4433 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVY2
#15: Protein 50S ribosomal protein L14 /


Mass: 13435.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplN, PA4253 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE5
#16: Protein 50S ribosomal protein L15 /


Mass: 15204.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplO, PA4244 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF4
#17: Protein 50S ribosomal protein L31 /


Mass: 7934.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmE, PA5049 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUD0
#18: Protein 50S ribosomal protein L16 /


Mass: 15434.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplP, PA4256 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE2
#19: Protein 50S ribosomal protein L17 /


Mass: 14533.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplQ, PA4237 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O52761
#20: Protein 50S ribosomal protein L18 /


Mass: 12687.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplR, PA4247 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF1
#21: Protein 50S ribosomal protein L19 /


Mass: 13055.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplS, PA3742 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXQ2
#22: Protein 50S ribosomal protein L20 /


Mass: 13397.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplT, PA2741 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I0A2
#23: Protein 50S ribosomal protein L21 /


Mass: 11678.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplU, PA4568 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL6
#25: Protein 50S ribosomal protein L23 /


Mass: 10969.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplW, PA4261 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD7
#26: Protein 50S ribosomal protein L24 /


Mass: 11494.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplX, PA4252 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE6
#27: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 21994.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplY, ctc, PA4671 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVC4
#28: Protein 50S ribosomal protein L27 /


Mass: 9010.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmA, PA4567 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVL7
#29: Protein 50S ribosomal protein L28 /


Mass: 9087.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmB, PA5316 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HTN8
#30: Protein 50S ribosomal protein L29 /


Mass: 7213.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmC, PA4255 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE3
#31: Protein 50S ribosomal protein L30 /


Mass: 6489.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpmD, PA4245 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF3

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RNA chain , 4 types, 4 molecules ABDta

#5: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 935990.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
#6: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38596.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Pseudomonas aeruginosa PAO1 (bacteria)
#9: RNA chain tRNA / Transfer RNA


Mass: 24485.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: modified bases were mutated to canonical ones. / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Pseudomonas aeruginosa PAO1 (bacteria)
#32: RNA chain 16S rRNA /


Mass: 494643.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Pseudomonas aeruginosa PAO1 (bacteria)

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Protein , 2 types, 2 molecules Sv

#24: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 11935.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rplV, PA4258 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE0
#53: Protein PHIKZ014


Mass: 43374.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q8SDE8

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

#33: Protein 30S ribosomal protein S2 /


Mass: 27376.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsB, PA3656 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O82850
#34: Protein 30S ribosomal protein S3 /


Mass: 25887.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsC, PA4257 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE1
#35: Protein 30S ribosomal protein S4 /


Mass: 23318.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsD, PA4239 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O52759
#36: Protein 30S ribosomal protein S5 /


Mass: 17650.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsE, PA4246 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF2
#37: Protein 30S ribosomal protein S6 /


Mass: 16189.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsF, PA4935 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUM9
#38: Protein 30S ribosomal protein S7 /


Mass: 17541.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsG, PA4267 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD1
#39: Protein 30S ribosomal protein S8 /


Mass: 14190.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsH, PA4249 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE9
#40: Protein 30S ribosomal protein S9 /


Mass: 14643.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsI, PA4432 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVY3
#41: Protein 30S ribosomal protein S10 /


Mass: 11786.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsJ, PA4264 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD4
#42: Protein 30S ribosomal protein S11 /


Mass: 13654.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsK, PA4240 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF8
#43: Protein 30S ribosomal protein S12 /


Mass: 13830.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsL, PA4268 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD0
#44: Protein 30S ribosomal protein S13 /


Mass: 13292.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsM, PA4241 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWF7
#45: Protein 30S ribosomal protein S14 /


Mass: 11591.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsN, PA4250 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE8
#46: Protein 30S ribosomal protein S15 /


Mass: 10135.661 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsO, PA4741 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HV58
#47: Protein 30S ribosomal protein S16 /


Mass: 9219.454 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsP, PA3745 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXP9
#48: Protein 30S ribosomal protein S17 /


Mass: 10106.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsQ, PA4254 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWE4
#49: Protein 30S ribosomal protein S18 /


Mass: 8892.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsR, PA4934 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HUN0
#50: Protein 30S ribosomal protein S19 /


Mass: 10382.331 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsS, PA4259 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HWD9
#51: Protein 30S ribosomal protein S20 /


Mass: 9942.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsT, PA4563 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HVM1
#52: Protein 30S ribosomal protein S21 /


Mass: 8508.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: rpsU, PA0579 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I5V8

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Non-polymers , 1 types, 171 molecules

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


Mass: 24.305 Da / Num. of mol.: 171 / Source method: obtained synthetically / Formula: Mg

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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: 70S-PHIKZ014 PHIKZ phage hijacked ribosome / Type: RIBOSOME / Entity ID: #1-#53 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1H2O (bacteria)
Source (recombinant)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Plasmid: pMiG41 - pJN105-H6-3C-PHIKZ014
Buffer solutionpH: 7.4
Details: 20 mM HEPES/KOH pH 7.5, 150 mM KCl, 16 mM MgCl2, 1 mM DTT, 0.1% TritonX100
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 5.16 sec. / Electron dose: 88.28 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8431
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
UCSF ChimeraX1.5/v9model building
EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
2crYOLO1.7.6.4image acquisition
4CTFFIND4CTF correction
7Coot0.9.8.1model fitting
9PHENIX1.20.1model refinement
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1852441
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169672 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028157126
ELECTRON MICROSCOPYf_angle_d0.7707234992
ELECTRON MICROSCOPYf_chiral_restr0.039529992
ELECTRON MICROSCOPYf_plane_restr0.00512693
ELECTRON MICROSCOPYf_dihedral_angle_d16.062561815

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