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- PDB-7unu: Pseudomonas aeruginosa 70S ribosome initiation complex bound to c... -

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Basic information

Entry
Database: PDB / ID: 7unu
TitlePseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (composite structure I-B)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • P-site initiator tRNA
  • Translation initiation factor IF-2
  • mRNA
KeywordsRIBOSOME / Initiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes
Function / homology
Function and homology information


translation initiation factor activity / translational initiation / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity ...translation initiation factor activity / translational initiation / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Putative DNA-binding domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 protein L11, N-terminal domain / Ribosomal L25p family / 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / 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 S3, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 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
Similarity search - Domain/homology
N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 ...N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Translation initiation factor IF-2 / 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 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / 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 / 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 speciesEscherichia coli (E. coli)
Pseudomonas aeruginosa PAO1 (bacteria)
Bacteriophage sp. (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBasu, R.S. / Sherman, M.B. / Gagnon, M.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136936 United States
Robert A. Welch FoundationH-2032-20200401 United States
CitationJournal: Nat Commun / Year: 2022
Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation
Authors: Basu, R.S. / Sherman, M.B. / Gagnon, M.G.
History
DepositionApr 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: 16S Ribosomal RNA
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: P-site initiator tRNA
w: mRNA
x: Translation initiation factor IF-2
A: 23S Ribosomal RNA
B: 5S Ribosomal RNA
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
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
L: 50S ribosomal protein L13
M: 50S ribosomal protein L14
N: 50S ribosomal protein L15
O: 50S ribosomal protein L16
P: 50S ribosomal protein L17
Q: 50S ribosomal protein L18
R: 50S ribosomal protein L19
S: 50S ribosomal protein L20
T: 50S ribosomal protein L21
U: 50S ribosomal protein L22
V: 50S ribosomal protein L23
W: 50S ribosomal protein L24
X: 50S ribosomal protein L25
Y: 50S ribosomal protein L27
Z: 50S ribosomal protein L28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L31
4: 50S ribosomal protein L32
5: 50S ribosomal protein L33
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,314,225668
Polymers2,298,72057
Non-polymers15,504611
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules avwAB

#1: RNA chain 16S Ribosomal RNA


Mass: 497973.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 1839535652
#22: RNA chain P-site initiator tRNA


Mass: 24846.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Initiator Methionine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBS-tRNAfMet / Production host: Escherichia coli HB101 (bacteria) / References: GenBank: 732678099
#23: RNA chain mRNA


Mass: 7804.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Bacteriophage sp. (virus)
#25: RNA chain 23S Ribosomal RNA


Mass: 937132.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 110227054
#26: RNA chain 5S Ribosomal RNA


Mass: 38596.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 1839535652

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

#2: Protein 30S ribosomal protein S2


Mass: 27376.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: O82850
#3: Protein 30S ribosomal protein S3


Mass: 25887.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE1
#4: Protein 30S ribosomal protein S4


Mass: 23318.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: O52759
#5: Protein 30S ribosomal protein S5


Mass: 17650.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF2
#6: Protein 30S ribosomal protein S6


Mass: 16189.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HUM9
#7: Protein 30S ribosomal protein S7


Mass: 17541.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD1
#8: Protein 30S ribosomal protein S8


Mass: 14190.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE9
#9: Protein 30S ribosomal protein S9


Mass: 14643.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVY3
#10: Protein 30S ribosomal protein S10


Mass: 11786.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD4
#11: Protein 30S ribosomal protein S11


Mass: 13654.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF8
#12: Protein 30S ribosomal protein S12


Mass: 13830.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD0
#13: Protein 30S ribosomal protein S13


Mass: 13292.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF7
#14: Protein 30S ribosomal protein S14


Mass: 11591.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE8
#15: Protein 30S ribosomal protein S15


Mass: 10135.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HV58
#16: Protein 30S ribosomal protein S16


Mass: 9219.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HXP9
#17: Protein 30S ribosomal protein S17


Mass: 10106.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE4
#18: Protein 30S ribosomal protein S18


Mass: 8892.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HUN0
#19: Protein 30S ribosomal protein S19


Mass: 10382.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD9
#20: Protein 30S ribosomal protein S20


Mass: 9942.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVM1
#21: Protein 30S ribosomal protein S21


Mass: 8508.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9I5V8

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Protein , 1 types, 1 molecules x

#24: Protein Translation initiation factor IF-2


Mass: 91049.641 Da / Num. of mol.: 1 / Fragment: N2 sub-domain of IF2
Source method: isolated from a genetically manipulated source
Details: Initiation Factor 2 / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: infB, PA4744 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q9HV55

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJLMNOPQRSTUVWXYZ12345678

#27: 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)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD8
#28: Protein 50S ribosomal protein L3


Mass: 22625.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD5
#29: Protein 50S ribosomal protein L4


Mass: 21673.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD6
#30: Protein 50S ribosomal protein L5


Mass: 20424.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE7
#31: Protein 50S ribosomal protein L6


Mass: 19129.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF0
#32: Protein 50S ribosomal protein L9


Mass: 15551.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HUN2
#33: Protein 50S ribosomal protein L10


Mass: 17657.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWC7
#34: Protein 50S ribosomal protein L11


Mass: 14925.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWC5
#35: Protein 50S ribosomal protein L13


Mass: 16058.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVY2
#36: Protein 50S ribosomal protein L14


Mass: 13435.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE5
#37: Protein 50S ribosomal protein L15


Mass: 15204.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF4
#38: Protein 50S ribosomal protein L16


Mass: 15434.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE2
#39: Protein 50S ribosomal protein L17


Mass: 14533.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: O52761
#40: Protein 50S ribosomal protein L18


Mass: 12687.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF1
#41: Protein 50S ribosomal protein L19


Mass: 13055.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HXQ2
#42: Protein 50S ribosomal protein L20


Mass: 13397.972 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9I0A2
#43: Protein 50S ribosomal protein L21


Mass: 11678.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVL6
#44: Protein 50S ribosomal protein L22


Mass: 11935.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: A0A1T1HVZ5
#45: Protein 50S ribosomal protein L23


Mass: 10969.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWD7
#46: Protein 50S ribosomal protein L24


Mass: 11494.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE6
#47: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 21994.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVC4
#48: Protein 50S ribosomal protein L27


Mass: 9010.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HVL7
#49: Protein 50S ribosomal protein L28


Mass: 9087.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HTN8
#50: Protein 50S ribosomal protein L29


Mass: 7213.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWE3
#51: Protein 50S ribosomal protein L30


Mass: 6489.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF3
#52: Protein 50S ribosomal protein L31


Mass: 7934.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HUD0
#53: Protein 50S ribosomal protein L32


Mass: 6807.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HZN4
#54: Protein 50S ribosomal protein L33


Mass: 6060.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HTN9
#55: Protein/peptide 50S ribosomal protein L34


Mass: 5226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: P29436
#56: 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: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9I0A1
#57: Protein/peptide 50S ribosomal protein L36


Mass: 4447.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9HWF6

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Non-polymers , 5 types, 812 molecules

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


Mass: 24.305 Da / Num. of mol.: 607 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#59: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#60: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#62: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (composite structure I-B)
Type: RIBOSOME / Entity ID: #1-#57 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28a
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1 sec. / Electron dose: 31 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8056

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.1.0particle selection
2EPU2.11.1image acquisition
4cryoSPARC3.1.0CTF correction
7Coot0.8.9.1model fitting
8UCSF Chimera1.14model fitting
10cryoSPARC3.1.0initial Euler assignment
11cryoSPARC3.1.0final Euler assignment
12cryoSPARC3.1.0classification
13cryoSPARC3.1.03D reconstruction
14PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 878576
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24614 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16SPG

6spg

16SPG1PDBexperimental model
23JCJ

3jcj

13JCJ2PDBexperimental model

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