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- PDB-9h9h: Complex 1 30S-IF1-IF2-IF3-GE81112 -

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Basic information

Entry
Database: PDB / ID: 9h9h
TitleComplex 1 30S-IF1-IF2-IF3-GE81112
Components
  • (Small ribosomal subunit protein ...) x 20
  • (Translation initiation factor IF- ...) x 3
  • 16S RNA (1534-MER)
  • mRNA (5'-R(P*AP*AP*UP*G)-3')
  • t-RNA (77-MER)
KeywordsRIBOSOME / Antibiotic / initiation factor / GE81112 / 30S
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / mRNA regulatory element binding translation repressor activity / response to cold / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / 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 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein S21 superfamily / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / 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 S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / : / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature.
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Translation initiation factor IF-2 / Small ribosomal subunit protein bS6 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Translation initiation factor IF-2 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSchedlbauer, A. / Han, X. / van Bakel, W. / Kaminishi, T. / Ochoa-Lizarralde, B. / Iturrioz, I. / Capuni, R. / Parry, R. / Zegarra, R. / Gil-Carton, D. ...Schedlbauer, A. / Han, X. / van Bakel, W. / Kaminishi, T. / Ochoa-Lizarralde, B. / Iturrioz, I. / Capuni, R. / Parry, R. / Zegarra, R. / Gil-Carton, D. / Lopez-Alonso, J.P. / Barragan Sanz, K. / Brandi, L. / Gualerzi, C.O. / Fucini, P. / Connell, S.R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-122705OB-I00 Spain
CitationJournal: bioRxiv / Year: 2024
Title: A binding site for the antibiotic GE81112 in the ribosomal mRNA channel.
Authors: Andreas Schedlbauer / Xu Han / Wouter van Bakel / Tatsuya Kaminishi / Borja Ochoa-Lizarralde / Idoia Iturrioz / Retina Çapuni / Ransford Parry / Ronny Zegarra / David Gil-Carton / Jorge P ...Authors: Andreas Schedlbauer / Xu Han / Wouter van Bakel / Tatsuya Kaminishi / Borja Ochoa-Lizarralde / Idoia Iturrioz / Retina Çapuni / Ransford Parry / Ronny Zegarra / David Gil-Carton / Jorge P López-Alonso / Kristina Barragan Sanz / Letizia Brandi / Claudio O Gualerzi / Paola Fucini / Sean R Connell /
Abstract: The initiation phase is the rate-limiting step of protein synthesis (translation) and is finely regulated, making it an important drug target. In bacteria, initiation is guided by three initiation ...The initiation phase is the rate-limiting step of protein synthesis (translation) and is finely regulated, making it an important drug target. In bacteria, initiation is guided by three initiation factors and involves positioning the start site on the messenger RNA within the P-site on the small ribosomal subunit (30S), where it is decoded by the initiator tRNA. This process can be efficiently inhibited by GE81112, a natural hydrophilic, noncyclic, nonribosomal tetrapeptide. It is found in nature in three structural variants (A, B and B1 with molecular masses of 643-658 Da). Previous biochemical and structural characterisation of GE81112 indicates that the primary mechanism of action of this antibiotic is to (1) prevent the initiator tRNA from binding correctly to the P-site and (2) block conformational rearrangements in initiation factor IF3, resulting in an 30S pre/C state. In this study, using cryoEM, we have determined the binding site of GE81112 in initiation complexes (3.2-3.7Å) and on empty ribosomes (2.09 Å). This binding site is within the mRNA channel (E-site) but remote from the binding site of the initiation factors and initiator tRNA. This suggests that it acts allosterically to prevent the initiator tRNA from being locked into place. The binding mode is consistent with previous biochemical studies and recent work identifying the key pharmacophores of GE81112.
History
DepositionOct 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: mRNA (5'-R(P*AP*AP*UP*G)-3')
3: t-RNA (77-MER)
A: 16S RNA (1534-MER)
B: Small ribosomal subunit protein uS2
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
X: Translation initiation factor IF-1
Y: Translation initiation factor IF-2
Z: Translation initiation factor IF-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)946,756185
Polymers942,15726
Non-polymers4,599159
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 23A

#1: RNA chain mRNA (5'-R(P*AP*AP*UP*G)-3')


Mass: 1264.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: RNA chain t-RNA (77-MER)


Mass: 24838.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 2208028712
#3: RNA chain 16S RNA (1534-MER)


Mass: 499873.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1758835854

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Small ribosomal subunit protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#4: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0
#5: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, b3314, JW3276 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V3
#6: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8
#7: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#8: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#9: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#10: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W7
#11: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7X3
#12: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5
#13: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#14: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3
#15: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S9
#16: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG59
#17: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#18: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T3
#19: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63
#20: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T7
#21: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U3
#22: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U7
#23: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli (E. coli) / References: UniProt: P68679

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Translation initiation factor IF- ... , 3 types, 3 molecules XYZ

#24: Protein Translation initiation factor IF-1


Mass: 8262.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infA, b0884, JW0867 / Production host: Escherichia coli (E. coli) / References: UniProt: P69222
#25: Protein Translation initiation factor IF-2


Mass: 97498.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infB, EcE24377A_3652 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZS65
#26: Protein Translation initiation factor IF-3


Mass: 20600.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infC, fit, srjA, b1718, JW5829 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A707

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Non-polymers , 4 types, 159 molecules

#27: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#28: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 152 / Source method: obtained synthetically / Formula: Mg
#29: Chemical ChemComp-A1IC4 / (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl-propanoic acid


Mass: 644.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34ClN9O10 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-ZN / ZINC ION


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

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Details

Has ligand of interestY
Has protein modificationN

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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: Complex 1 30S-IF1-IF2-IF3-GE81112 / Type: RIBOSOME / Entity ID: #1-#26 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
4CTFFINDCTF correction
5RELIONCTF correction
8UCSF ChimeraXmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 232679
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46163 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4YBB

4ybb


Accession code: 4YBB / Source name: PDB / Type: experimental model

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