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- PDB-4uy8: Molecular basis for the ribosome functioning as a L-tryptophan se... -

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Entry
Database: PDB / ID: 4uy8
TitleMolecular basis for the ribosome functioning as a L-tryptophan sensor - Cryo-EM structure of a TnaC stalled E.coli ribosome
Components
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • RIBOSOMAL L7 PROTEIN
  • RIBOSOMAL PROTEIN L9
  • RNA
  • RRNA-23S RIBOSOMAL RNA
  • RRNA-5S RIBOSOMAL RNA
  • TRYPTOPHANASE
KeywordsRIBOSOME / TNAC / TRANSLATION REGULATION
Function / homology
Function and homology information


positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / t-UTP complex / rDNA heterochromatin / tryptophan catabolic process / rRNA methylation / positive regulation of transcription by RNA polymerase I / stringent response / Major pathway of rRNA processing in the nucleolus and cytosol / transcriptional attenuation ...positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / t-UTP complex / rDNA heterochromatin / tryptophan catabolic process / rRNA methylation / positive regulation of transcription by RNA polymerase I / stringent response / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / small-subunit processome / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / : / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Ribosomal protein L28/L24 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Ribosomal Protein L9; domain 1 / Helix Hairpins - #3980 ...Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Ribosomal protein L28/L24 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Ribosomal Protein L9; domain 1 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / RRM (RNA recognition motif) domain / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Single Sheet / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Nucleic acid-binding proteins / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / 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 L11, N-terminal / 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 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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / 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
Similarity search - Domain/homology
TRYPTOPHAN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / U3 small nucleolar RNA-associated protein 5 / Large ribosomal subunit protein bL28 ...TRYPTOPHAN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / U3 small nucleolar RNA-associated protein 5 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L3 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / : / 50S ribosomal protein L10 / 50S ribosomal protein L22 / : / 50S ribosomal protein L25 / : / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / 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 / Large ribosomal subunit protein uL13 / Tryptophanase operon leader peptide / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / 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 / Large ribosomal subunit protein bL25 / : / : / L8 / : / : / : / : / : / : / : / : / : / : / : / : / : / : / :
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBischoff, L. / Berninghausen, O. / Beckmann, R.
CitationJournal: Cell Rep / Year: 2014
Title: Molecular basis for the ribosome functioning as an L-tryptophan sensor.
Authors: Lukas Bischoff / Otto Berninghausen / Roland Beckmann /
Abstract: Elevated levels of the free amino acid L-tryptophan (L-Trp) trigger expression of the tryptophanase tnaCAB operon in E. coli. Activation depends on tryptophan-dependent ribosomal stalling during ...Elevated levels of the free amino acid L-tryptophan (L-Trp) trigger expression of the tryptophanase tnaCAB operon in E. coli. Activation depends on tryptophan-dependent ribosomal stalling during translation of the upstream TnaC peptide. Here, we present a cryoelectron microscopy (cryo-EM) reconstruction at 3.8 Å resolution of a ribosome stalled by the TnaC peptide. Unexpectedly, we observe two L-Trp molecules in the ribosomal exit tunnel coordinated within composite hydrophobic pockets formed by the nascent TnaC peptide and the tunnel wall. As a result, the peptidyl transferase center (PTC) adopts a distinct conformation that precludes productive accommodation of release factor 2 (RF2), thereby inducing translational stalling. Collectively, our results demonstrate how the translating ribosome can act as a small molecule sensor for gene regulation.
History
DepositionAug 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Source and taxonomy / Structure summary
Category: em_image_scans / entity / entity_src_nat / Item: _entity.src_method / _entity_src_nat.strain
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations
Category: diffrn_radiation / diffrn_radiation_wavelength ...diffrn_radiation / diffrn_radiation_wavelength / em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
0: 50S RIBOSOMAL PROTEIN L32
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
5: 50S RIBOSOMAL PROTEIN L10
6: RIBOSOMAL L7 PROTEIN
7: TRYPTOPHANASE
8: 50S RIBOSOMAL PROTEIN L25
A: RRNA-23S RIBOSOMAL RNA
B: RRNA-5S RIBOSOMAL RNA
C: 50S RIBOSOMAL PROTEIN L2
D: 50S RIBOSOMAL PROTEIN L3
E: 50S RIBOSOMAL PROTEIN L4
F: 50S RIBOSOMAL PROTEIN L5
G: 50S RIBOSOMAL PROTEIN L6
H: RIBOSOMAL PROTEIN L9
I: 50S RIBOSOMAL PROTEIN L11
J: 50S RIBOSOMAL PROTEIN L13
K: 50S RIBOSOMAL PROTEIN L14
L: 50S RIBOSOMAL PROTEIN L15
M: 50S RIBOSOMAL PROTEIN L16
N: 50S RIBOSOMAL PROTEIN L17
O: 50S RIBOSOMAL PROTEIN L18
P: 50S RIBOSOMAL PROTEIN L19
Q: 50S RIBOSOMAL PROTEIN L20
R: 50S RIBOSOMAL PROTEIN L21
S: 50S RIBOSOMAL PROTEIN L22
T: 50S RIBOSOMAL PROTEIN L23
U: 50S RIBOSOMAL PROTEIN L24
V: RNA
W: 50S RIBOSOMAL PROTEIN L27
X: 50S RIBOSOMAL PROTEIN L28
Y: 50S RIBOSOMAL PROTEIN L29
Z: 50S RIBOSOMAL PROTEIN L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,376,256181
Polymers1,372,30635
Non-polymers3,949146
Water7,909439
1


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

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Components

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50S RIBOSOMAL PROTEIN ... , 29 types, 29 molecules 0123458CDEFGIJKLMNOPQRSTUWXYZ

#1: 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: KC6 / References: UniProt: U5SG25, UniProt: P0A7N4*PLUS
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-53 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: U5SML7, UniProt: P0A7N9*PLUS
#3: 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: KC6 / References: UniProt: P0A7P5
#4: 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: KC6 / References: UniProt: W0KX84, UniProt: P0A7Q1*PLUS
#5: 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: KC6 / References: UniProt: X7QRM8, UniProt: P0A7Q6*PLUS
#6: Protein 50S RIBOSOMAL PROTEIN L10 /


Mass: 15981.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: E1IXH4, UniProt: P0A7J3*PLUS
#9: 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: KC6 / References: UniProt: E3PCX7, UniProt: P68919*PLUS
#12: 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: KC6 / References: UniProt: X7QS81, UniProt: P60422*PLUS
#13: 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: KC6 / References: UniProt: D6IEL8, UniProt: P60438*PLUS
#14: 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: KC6 / References: UniProt: X7QRP4, UniProt: P60723*PLUS
#15: 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: KC6 / References: UniProt: X7QU92, UniProt: P62399*PLUS
#16: 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: KC6 / References: UniProt: X7QBP9, UniProt: P0AG55*PLUS
#18: 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: KC6 / References: UniProt: E7HV64, UniProt: P0A7J7*PLUS
#19: 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: KC6 / References: UniProt: X7QR95, UniProt: P0AA10*PLUS
#20: 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: KC6 / References: UniProt: E1PGS6, UniProt: P0ADY3*PLUS
#21: 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: KC6 / References: UniProt: P02413
#22: 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: KC6 / References: UniProt: D7XL00, UniProt: P0ADY7*PLUS
#23: 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: KC6 / References: UniProt: X7QRM3, UniProt: P0AG44*PLUS
#24: 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: KC6 / References: UniProt: X7QRN2, UniProt: P0C018*PLUS
#25: 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: KC6 / References: UniProt: X7R0V6, UniProt: P0A7K6*PLUS
#26: 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: KC6 / References: UniProt: X7QXR5, UniProt: P0A7L3*PLUS
#27: 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: KC6 / References: UniProt: W0L2B9, UniProt: P0AG48*PLUS
#28: 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: KC6 / References: UniProt: E1JB10, UniProt: P61175*PLUS
#29: 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: KC6 / References: UniProt: C6EGE8, UniProt: P0ADZ0*PLUS
#30: 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: KC6 / References: UniProt: W0L2N0, UniProt: P60624*PLUS
#32: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 8476.680 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-85 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: W0KYJ4, UniProt: P0A7L8*PLUS
#33: 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: KC6 / References: UniProt: C3SME2, UniProt: P0A7M2*PLUS
#34: 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: KC6 / References: UniProt: D7X2Z3, UniProt: P0A7M6*PLUS
#35: 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: KC6 / References: UniProt: W0L301, UniProt: P0AG51*PLUS

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Protein/peptide , 3 types, 3 molecules 67H

#7: Protein/peptide RIBOSOMAL L7 PROTEIN


Mass: 3300.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: V5UZV4, UniProt: P0A7K2*PLUS
#8: Protein/peptide TRYPTOPHANASE /


Mass: 2427.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: A4GWE7, UniProt: P0AD89*PLUS
#17: Protein/peptide RIBOSOMAL PROTEIN L9 /


Mass: 5467.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: UniProt: D8BKG3, UniProt: P0A7R1*PLUS

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RNA chain , 3 types, 3 molecules ABV

#10: RNA chain RRNA-23S RIBOSOMAL RNA


Mass: 925492.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: GenBank: 64682453
#11: RNA chain RRNA-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: KC6 / References: GenBank: 64693170
#31: RNA chain RNA /


Mass: 24890.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: KC6 / References: GenBank: 66001753

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Non-polymers , 4 types, 585 molecules

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


Mass: 24.305 Da / Num. of mol.: 143 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#38: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#39: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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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: TNAC STALLED E.COLI RIBOSOME / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 --CRYOGEN- ETHANE,INSTRUMENT- FEI VITROBOT MARK IV

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 27, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Num. of particles: 72468
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2773. (DEPOSITION ID: 12802).
Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26922 65452 174 439 92987

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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