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- PDB-7n2v: Elongating 70S ribosome complex in a spectinomycin-stalled interm... -

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Basic information

Entry
Database: PDB / ID: 7n2v
TitleElongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • (tRNA) x 2
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Elongation factor G
  • Nascent peptide
  • mRNA
KeywordsRIBOSOME / Elongation complex / tRNA / mRNA / translocation / EF-G & GTP
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation ...negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / translational termination / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / translational initiation / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / 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 / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L10 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Elongation factor Tu domain 2 / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 1,4-DIAMINOBUTANE / SPECTINOMYCIN / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 1,4-DIAMINOBUTANE / SPECTINOMYCIN / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Elongation factor G / 30S ribosomal protein S12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / 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 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsRundlet, E.J. / Holm, M. / Schacherl, M. / Natchiar, K.S. / Altman, R.B. / Spahn, C.M.T. / Myasnikov, A.G. / Blanchard, S.C.
CitationJournal: Nature / Year: 2021
Title: Structural basis of early translocation events on the ribosome.
Authors: Emily J Rundlet / Mikael Holm / Magdalena Schacherl / S Kundhavai Natchiar / Roger B Altman / Christian M T Spahn / Alexander G Myasnikov / Scott C Blanchard /
Abstract: Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around ...Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10 to 10 at each step) over thousands of cycles. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
16: 16S rRNA
SB: 30S ribosomal protein S2
SC: 30S ribosomal protein S3
SD: 30S ribosomal protein S4
SE: 30S ribosomal protein S5
SF: 30S ribosomal protein S6
SG: 30S ribosomal protein S7
SH: 30S ribosomal protein S8
SI: 30S ribosomal protein S9
SJ: 30S ribosomal protein S10
SK: 30S ribosomal protein S11
SL: 30S ribosomal protein S12
SM: 30S ribosomal protein S13
SN: 30S ribosomal protein S14
SO: 30S ribosomal protein S15
SP: 30S ribosomal protein S16
SQ: 30S ribosomal protein S17
SR: 30S ribosomal protein S18
SS: 30S ribosomal protein S19
ST: 30S ribosomal protein S20
SU: 30S ribosomal protein S21
mR: mRNA
23: 23S rRNA
5: 5S rRNA
LB: 50S ribosomal protein L2
LC: 50S ribosomal protein L3
LD: 50S ribosomal protein L4
LE: 50S ribosomal protein L5
LF: 50S ribosomal protein L6
LI: 50S ribosomal protein L9
LJ: 50S ribosomal protein L10
LK: 50S ribosomal protein L11
LM: 50S ribosomal protein L13
LN: 50S ribosomal protein L14
LO: 50S ribosomal protein L15
LP: 50S ribosomal protein L16
LQ: 50S ribosomal protein L17
LR: 50S ribosomal protein L18
LS: 50S ribosomal protein L19
LT: 50S ribosomal protein L20
LU: 50S ribosomal protein L21
LV: 50S ribosomal protein L22
LW: 50S ribosomal protein L23
LX: 50S ribosomal protein L24
LY: 50S ribosomal protein L25
La: 50S ribosomal protein L27
Lb: 50S ribosomal protein L28
Lc: 50S ribosomal protein L29
Ld: 50S ribosomal protein L30
Le: 50S ribosomal protein L31
Lf: 50S ribosomal protein L32
Lg: 50S ribosomal protein L33
Lh: 50S ribosomal protein L34
Li: 50S ribosomal protein L35
Lj: 50S ribosomal protein L36
EF: Elongation factor G
Pp: Nascent peptide
Pt: tRNA
Dt: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,349,540431
Polymers2,336,65959
Non-polymers12,881372
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules 16mR235PtDt

#1: RNA chain 16S rRNA


Mass: 497391.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: GenBank: 1789840096
#22: RNA chain mRNA


Mass: 19128.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA / Source: (synth.) Escherichia coli BL21 (bacteria)
#23: RNA chain 23S rRNA


Mass: 941812.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600
#24: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5S rRNA / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: GenBank: 991970073
#58: RNA chain tRNA


Mass: 34369.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNA / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MRE600 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MRE600
#59: RNA chain tRNA


Mass: 34451.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNA / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MRE600 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MRE600

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

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


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S2 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7V3
#4: Protein 30S ribosomal protein S4 / Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S4 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S5 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S6 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P02358
#7: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S7 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P02359
#8: Protein 30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S8 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S9 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S10 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7R5
#11: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S11 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S12 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: A0A4S5B3M5
#13: Protein 30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S13 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S14 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S15 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0ADZ4
#16: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S16 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7T3
#17: Protein 30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S17 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S18 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S19 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7U3
#20: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S20 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S21 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P68679

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

#25: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L2 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P60422
#26: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L3 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P60438
#27: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L4 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P60723
#28: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L5 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P62399
#29: Protein 50S ribosomal protein L6 / Large ribosomal subunit protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L6 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG55
#30: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L9 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7R1
#31: Protein 50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L10 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7J3
#32: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L11 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7J7
#33: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L13 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AA10
#34: Protein 50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L14 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0ADY3
#35: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L15 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P02413
#36: Protein 50S ribosomal protein L16


Mass: 15327.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L16 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0ADY7
#37: Protein 50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L17 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG44
#38: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L18 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0C018
#39: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L19 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7K6
#40: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L20 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7L3
#41: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L21 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG48
#42: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L22 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P61175
#43: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L23 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0ADZ0
#44: Protein 50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L24 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P60624
#45: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L25 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P68919
#46: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L27 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7L8
#47: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L28 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7M2
#48: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L29 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7M6
#49: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L30 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0AG51
#50: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L31 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7M9
#51: Protein 50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L32 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7N4
#52: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L33 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7N9
#53: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L34 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7P5
#54: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L35 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7Q1
#55: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L36 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: UniProt: P0A7Q6

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Protein / Protein/peptide , 2 types, 2 molecules EFPp

#56: Protein Elongation factor G / EF-G


Mass: 77632.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Elongation factor (EF-G) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MRE600 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MRE600 / References: UniProt: A0A0H3PU63
#57: Protein/peptide Nascent peptide


Mass: 425.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Nascent peptide / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600

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Non-polymers , 8 types, 398 molecules

#60: Chemical ChemComp-SCM / SPECTINOMYCIN / ACTINOSPECTACIN / ESPECTINOMICINA / CHX-3101


Mass: 332.350 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H24N2O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#61: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 344 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#63: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#64: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#65: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#66: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#67: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1)
Type: RIBOSOME / Entity ID: #1-#56, #58, #57, #59 / Source: NATURAL
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 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 FIELD
Image recordingElectron dose: 87 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33688 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL

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