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- PDB-4v6t: Structure of the bacterial ribosome complexed by tmRNA-SmpB and E... -

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Basic information

Entry
Database: PDB / ID: 4v6t
TitleStructure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • SsrA-binding protein
  • elongation factor GEF-G
  • formyl-methionine specific initiator transfer RNA
  • full length transfer messenger RNA (tmRNA)
KeywordsRIBOSOME / trans-translation / MLD-loading / translocation
Function / homology
Function and homology information


stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / : / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / ribosome biogenesis / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / molecular adaptor activity / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / 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 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 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 / 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 (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsRamrath, D.J.F. / Yamamoto, H. / Rother, K. / Wittek, D. / Pech, M. / Mielke, T. / Loerke, J. / Scheerer, P. / Ivanov, P. / Teraoka, Y. ...Ramrath, D.J.F. / Yamamoto, H. / Rother, K. / Wittek, D. / Pech, M. / Mielke, T. / Loerke, J. / Scheerer, P. / Ivanov, P. / Teraoka, Y. / Shpanchenko, O. / Nierhaus, K.H. / Spahn, C.M.T.
CitationJournal: Nature / Year: 2012
Title: The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
Authors: David J F Ramrath / Hiroshi Yamamoto / Kristian Rother / Daniela Wittek / Markus Pech / Thorsten Mielke / Justus Loerke / Patrick Scheerer / Pavel Ivanov / Yoshika Teraoka / Olga Shpanchenko ...Authors: David J F Ramrath / Hiroshi Yamamoto / Kristian Rother / Daniela Wittek / Markus Pech / Thorsten Mielke / Justus Loerke / Patrick Scheerer / Pavel Ivanov / Yoshika Teraoka / Olga Shpanchenko / Knud H Nierhaus / Christian M T Spahn /
Abstract: Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation. The SmpB protein forms a complex with the ...Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation. The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmRNA then enters the A site of the ribosome. Subsequently, the TLD-SmpB module is translocated to the P site, a process that is facilitated by the elongation factor EF-G, and translation is switched to the mRNA-like domain (MLD) of the tmRNA. Accurate loading of the MLD into the mRNA path is an unusual initiation mechanism. Despite various snapshots of different ribosome-tmRNA complexes at low to intermediate resolution, it is unclear how the large, highly structured tmRNA is translocated and how the MLD is loaded. Here we present a cryo-electron microscopy reconstruction of a fusidic-acid-stalled ribosomal 70S-tmRNA-SmpB-EF-G complex (carrying both of the large ligands, that is, EF-G and tmRNA) at 8.3 Å resolution. This post-translocational intermediate (TI(POST)) presents the TLD-SmpB module in an intrasubunit ap/P hybrid site and a tRNA(fMet) in an intrasubunit pe/E hybrid site. Conformational changes in the ribosome and tmRNA occur in the intersubunit space and on the solvent side. The key underlying event is a unique extra-large swivel movement of the 30S head, which is crucial for both tmRNA-SmpB translocation and MLD loading, thereby coupling translocation to MLD loading. This mechanism exemplifies the versatile, dynamic nature of the ribosome, and it shows that the conformational modes of the ribosome that normally drive canonical translation can also be used in a modified form to facilitate more complex tasks in specialized non-canonical pathways.
History
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J18, 3J19
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 1, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 2.0Dec 18, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
AV: full length transfer messenger RNA (tmRNA)
AW: SsrA-binding protein
AX: formyl-methionine specific initiator transfer RNA
AY: elongation factor G
BA: 23S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
BB: 5S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)2,348,61356
Polymers2,348,61356
Non-polymers00
Water0
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 AAAVAXBABB

#1: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: GenBank: NC_000913
#22: RNA chain full length transfer messenger RNA (tmRNA)


Mass: 117212.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: NC_000913
#24: RNA chain formyl-methionine specific initiator transfer RNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: NC_000913
#26: RNA chain 23S ribosomal RNA /


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: GenBank: NC_000913
#56: RNA chain 5S ribosomal RNA /


Mass: 38483.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: GenBank: NC_000913

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

#2: Protein 30S ribosomal protein S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7V3
#4: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5 /


Mass: 15804.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P02358
#7: Protein 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P02359
#8: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7R5
#11: Protein 30S ribosomal protein S11 /


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7S3
#13: Protein 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0ADZ4
#16: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7T3
#17: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18 /


Mass: 6466.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7U3
#20: Protein 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21 /


Mass: 6067.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P68679

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Protein , 2 types, 2 molecules AWAY

#23: Protein SsrA-binding protein


Mass: 14177.479 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pGEMEX-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#25: Protein elongation factor G / EF-G / EF-G


Mass: 76977.102 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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50S ribosomal protein ... , 29 types, 29 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB0B1B2B3B4

#27: Protein 50S ribosomal protein L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P60422
#28: Protein 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P60438
#29: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P60723
#30: Protein 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P62399
#31: Protein 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG55
#32: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7R1
#33: Protein 50S ribosomal protein L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7J7
#34: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AA10
#35: Protein 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0ADY3
#36: Protein 50S ribosomal protein L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P02413
#37: Protein 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0ADY7
#38: Protein 50S ribosomal protein L17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG44
#39: Protein 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0C018
#40: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7K6
#41: Protein 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7L3
#42: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG48
#43: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P61175
#44: Protein 50S ribosomal protein L23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0ADZ0
#45: Protein 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P60624
#46: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P68919
#47: Protein 50S ribosomal protein L27 /


Mass: 8275.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7L8
#48: Protein 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7M2
#49: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7M6
#50: Protein 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0AG51
#51: Protein 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7N4
#52: Protein/peptide 50S ribosomal protein L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7N9
#53: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7P5
#54: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7Q1
#55: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CAN20 / References: UniProt: P0A7Q6

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Details

Sequence detailsMODELED SEQUENCES FOR SSRA_BINDING PROTEIN (UNP Q8RR57 RESIDUES 1-123) AND ELONGATION FACTOR G (UNP ...MODELED SEQUENCES FOR SSRA_BINDING PROTEIN (UNP Q8RR57 RESIDUES 1-123) AND ELONGATION FACTOR G (UNP Q5SHN5 1-691) ARE FROM THERMUS THERMOPHILUS.

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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: Ribosomal complex 70S-tmRNA-SmpB-tRNA-EFG-GDP-FA / Type: RIBOSOME / Details: in vitro reconstituted ribosomal complex
Buffer solutionpH: 7.6
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R3-3 Cu mesh with 2 nm carbon support film
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 96.15 K / Humidity: 100 %
Details: blot for 5-10 seconds before plunging into liquid ethane (FEI Vitrobot)
Method: blot for 5-10 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 8, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 302
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: The volumes were CTF-corrected in defocus groups, with an average of approximately 215 individual images per group
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: angular refinement / Resolution: 8.3 Å / Num. of particles: 68843 / Nominal pixel size: 1.26 Å / Actual pixel size: 1.26 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms24762 41770 0 0 66532

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