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- PDB-4v74: 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation ... -

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Basic information

Entry
Database: PDB / ID: 4v74
Title70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'
  • 5S ribosomal RNA
  • fMet-Val-tRNA-Val
  • tRNA-fMet
KeywordsRIBOSOME / cryo-EM refinement / tRNA / translocation intermediate
Function / homology
Function and homology information


stringent response / mRNA base-pairing post-transcriptional repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / transcription antitermination factor activity, RNA binding / RNA folding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity ...stringent response / mRNA base-pairing post-transcriptional repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / transcription antitermination factor activity, RNA binding / RNA folding / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / four-way junction DNA binding / assembly of large subunit precursor of preribosome / negative regulation of translational initiation / mature ribosome assembly / maturation of LSU-rRNA / translational termination / mRNA regulatory element binding translation repressor activity / regulation of mRNA stability / transcription antitermination / polysomal ribosome / positive regulation of RNA splicing / endodeoxyribonuclease activity / ribosome assembly / DNA-templated transcription, termination / maintenance of translational fidelity / response to reactive oxygen species / positive regulation of translational fidelity / regulation of cell growth / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / regulation of translation / ribosome binding / ribosome biogenesis / response to radiation / cytosolic large ribosomal subunit / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16 signature. / Ribosomal protein S16, conserved site / Ribosomal protein S21 / Ribosomal protein L11, bacterial-type / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L11 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L32p, bacterial type / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11/L12 / 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 L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L33 signature. / Ribosomal protein L9 / Ribosomal protein L33, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S2 signature 2. / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal L28 family / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L30, bacterial-type / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily
Similarity search - Domain/homology
50S ribosomal protein L17 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S3 / 30S ribosomal protein S2 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 ...50S ribosomal protein L17 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S3 / 30S ribosomal protein S2 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 30S ribosomal protein S19 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L5 / 50S ribosomal protein L22 / 50S ribosomal protein L4 / 50S ribosomal protein L24 / 30S ribosomal protein S21 / 30S ribosomal protein S20 / N-FORMYLMETHIONINE / 30S ribosomal protein S18 / 50S ribosomal protein L20 / VALINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L1 / 50S ribosomal protein L27 / 30S ribosomal protein S16 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsBlau, C. / Bock, L.V. / Schroder, G.F. / Davydov, I. / Fischer, N. / Stark, H. / Rodnina, M.V. / Vaiana, A.C. / Grubmuller, H.
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Energy barriers and driving forces in tRNA translocation through the ribosome.
Authors: Lars V Bock / Christian Blau / Gunnar F Schröder / Iakov I Davydov / Niels Fischer / Holger Stark / Marina V Rodnina / Andrea C Vaiana / Helmut Grubmüller /
Abstract: During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics ...During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J57, 3J58
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 8, 2015Group: Other
Revision 2.0Jul 18, 2018Group: Data collection / Polymer sequence / Category: em_image_scans / em_software / entity_poly
Item: _em_software.image_processing_id / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Sep 5, 2018Group: Data collection / Experimental preparation / Refinement description
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / exptl / refine / refine_hist
Item: _exptl.crystals_number
Revision 2.2Dec 18, 2019Group: Database references / Derived calculations / Other / Category: atom_sites / struct_conn / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
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
AA: 16S ribosomal RNA
A1: fMet-Val-tRNA-Val
A2: 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'
A3: tRNA-fMet
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
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
B5: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,195,47158
Polymers2,195,17756
Non-polymers2942
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein 30S ribosomal protein S2 /


Mass: 24277.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V0
#2: Protein 30S ribosomal protein S3 /


Mass: 23207.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V3
#3: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V8
#4: Protein 30S ribosomal protein S5 /


Mass: 15828.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W1
#5: Protein 30S ribosomal protein S6 /


Mass: 11667.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02358
#6: Protein 30S ribosomal protein S7 /


Mass: 16788.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02359
#7: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7W7
#8: Protein 30S ribosomal protein S9 /


Mass: 14580.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7X3
#9: Protein 30S ribosomal protein S10 /


Mass: 11221.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R5
#10: Protein 30S ribosomal protein S11 /


Mass: 12513.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R9
#11: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S3
#12: Protein 30S ribosomal protein S13 /


Mass: 12657.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S9
#13: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG59
#14: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADZ4
#15: Protein 30S ribosomal protein S16 /


Mass: 9063.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T3
#16: Protein 30S ribosomal protein S17 /


Mass: 9287.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG63
#17: Protein 30S ribosomal protein S18 /


Mass: 6490.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7T7
#18: Protein 30S ribosomal protein S19 /


Mass: 9081.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U3
#19: Protein 30S ribosomal protein S20 /


Mass: 9532.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U7
#20: Protein 30S ribosomal protein S21 /


Mass: 6091.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P68679

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RNA chain , 6 types, 6 molecules AAA1A2A3BABB

#21: RNA chain 16S ribosomal RNA /


Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#22: RNA chain fMet-Val-tRNA-Val


Mass: 24617.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#23: RNA chain 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'


Mass: 4693.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA
#24: RNA chain tRNA-fMet


Mass: 24848.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
#54: 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: K12
#55: RNA chain 5S ribosomal RNA /


Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12

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50S ribosomal protein ... , 30 types, 30 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB0B1B2B3B4B5

#25: Protein 50S ribosomal protein L2 /


Mass: 29792.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P60422
#26: 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: K12 / References: UniProt: P60438
#27: 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: K12 / References: UniProt: P60723
#28: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P62399
#29: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG55
#30: 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: K12 / References: UniProt: P0A7R1
#31: Protein 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7J7
#32: 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: K12 / References: UniProt: P0AA10
#33: Protein 50S ribosomal protein L14 /


Mass: 13449.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADY3
#34: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02413
#35: 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: K12 / References: UniProt: P0ADY7
#36: Protein 50S ribosomal protein L17 /


Mass: 13719.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG44
#37: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0C018
#38: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7K6
#39: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7L3
#40: 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: K12 / References: UniProt: P0AG48
#41: 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: K12 / References: UniProt: P61175
#42: Protein 50S ribosomal protein L23 /


Mass: 10544.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADZ0
#43: Protein 50S ribosomal protein L24 /


Mass: 11208.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P60624
#44: 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: K12 / References: UniProt: P68919
#45: Protein 50S ribosomal protein L27 /


Mass: 8502.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7L8
#46: Protein 50S ribosomal protein L28 /


Mass: 9053.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7M2
#47: 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: K12 / References: UniProt: P0A7M6
#48: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG51
#49: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7N4
#50: Protein 50S ribosomal protein L33 /


Mass: 5838.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7N9
#51: 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: K12 / References: UniProt: P0A7P5
#52: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7Q1
#53: 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: K12 / References: UniProt: P0A7Q6
#56: Protein 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7L0

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Non-polymers , 2 types, 2 molecules

#57: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#58: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S

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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: E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex / Type: RIBOSOME
Buffer solutionName: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
pH: 7.5
Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 75 %
Details: Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
Method: Manual blotting for about 2 seconds
Time resolved state: Samples were vitrified at different time points along the reaction coordinate (1, 2, 5 and 20 minutes after addition of deacylated tRNAfMet to 70S-fMetVal-tRNAVal complexes).

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: May 11, 2008
Details: Objective lens astigmatism was corrected at 200,000 times magnification
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 161000 X / Calibrated magnification: 162740 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS (4k x 4k) / Details: 4k CCD camera (TVIPS)

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Processing

EM software
IDNameCategory
1DireXmodel fitting
2Custom3D reconstruction
3IMAGIC3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: local
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection matching / Resolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3052 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.8 Å
Details: Final maps were calculated from 13 datasets acquired at different time points, computationally sorted into distinct substates.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--Cross-correlation gradient based REFINEMENT PROTOCOL--flexible fitting, dynamic elastic network
Atomic model building
IDPDB-ID 3D fitting-ID
13I1O

3i1o
PDB Unreleased entry

1
22K4C1
32HGP

2hgp
PDB Unreleased entry

1
42WRI

2wri
PDB Unreleased entry

1

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