[English] 日本語
Yorodumi
- EMDB-12035: E. coli 70S containing suppressor tRNA in the A-site stabilized b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12035
TitleE. coli 70S containing suppressor tRNA in the A-site stabilized by a Negamycin analogue and P-site tRNA-nascent chain.
Map data
Sample70S ribosome with A,P,E-site tRNA:
mRNAMessenger RNA / (nucleic-acidNucleic acid) x 7 / (50S ribosomal protein ...) x 29 / (30S ribosomal protein ...) x 20 / ermC Nacent chain / (ligand) x 4
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / four-way junction DNA binding / negative regulation of translational initiation / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / translational initiation / polysomal ribosome / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / ribosome assembly / endodeoxyribonuclease activity / DNA-templated transcription, termination / positive regulation of translational fidelity / maintenance of translational fidelity / response to reactive oxygen species / 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 / regulation of mRNA stability / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal large subunit assembly / ribosome biogenesis / response to radiation / 5S rRNA binding / small ribosomal subunit / cytosolic 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
Similarity search - Function
Ribosomal protein S21 signature. / Ribosomal protein S21, conserved site / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein S21 superfamily ...Ribosomal protein S21 signature. / Ribosomal protein S21, conserved site / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein S16 signature. / Ribosomal protein S16, conserved site / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L19 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9, N-terminal / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6 signature. / Ribosomal protein S6, conserved site / Ribosomal protein L14P, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L34 / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal L28 family / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L33 / Ribosomal protein L34 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S18 signature. / Ribosomal protein S18, conserved site / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / L28p-like / Ribosomal L32p protein family / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L16
Similarity search - Domain/homology
50S ribosomal protein L30 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 50S ribosomal protein L21 ...50S ribosomal protein L30 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L2 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 30S ribosomal protein S4 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S3 / 50S ribosomal protein L32 / 30S ribosomal protein S2 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L31 / 50S ribosomal protein L33 / 30S ribosomal protein S20 / 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 S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAlbers S / Beckert B / Matthies M / Schuster R / Riedner M / Seuring C / Sanyal S / Torda A / Wilson ND / Ignatova Z
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2021
Title: Harnessing evolutionarily flexibility in tRNAs to maximize nonsense suppression activities
Authors: Albers S / Beckert B / Wilson ND / Ignatova Z
History
DepositionDec 3, 2020-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b5k
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_12035.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 345.6 Å
0.96 Å/pix.
x 360 pix.
= 345.6 Å
0.96 Å/pix.
x 360 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density
Contour LevelBy AUTHOR: 0.083 / Movie #1: 0.07
Minimum - Maximum-0.18944913 - 0.4477828
Average (Standard dev.)0.004087359 (±0.017508617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.960.960.96
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1890.4480.004

-
Supplemental data

+
Additional map: Multi body LSU

Fileemd_12035_additional_1.map
AnnotationMulti body LSU
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

+
Additional map: Multi body SSU-body

Fileemd_12035_additional_2.map
AnnotationMulti body SSU-body
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

+
Additional map: Multi body SSU-head

Fileemd_12035_additional_3.map
AnnotationMulti body SSU-head
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

+
Additional map: relion final 3D refine

Fileemd_12035_additional_4.map
Annotationrelion final 3D refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

+
Half map: half map 1

Fileemd_12035_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

+
Half map: half map 2

Fileemd_12035_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire 70S ribosome with A,P,E-site tRNA

EntireName: 70S ribosome with A,P,E-site tRNA / Number of Components: 64

+
Component #1: protein, 70S ribosome with A,P,E-site tRNA

ProteinName: 70S ribosome with A,P,E-site tRNA / Recombinant expression: No

+
Component #2: protein, 70S ribosome with A,P,E-site tRNA

ProteinName: 70S ribosome with A,P,E-site tRNA / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #3: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)
Source (engineered)Expression System: synthetic construct (others)

+
Component #4: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU ...Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAU(1MG)(PSU)(5MU)GAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCACUUA CCAACCCGAU GCAAACUGCG AAUACCGGAG AAUGUUAUCA CGGGAGACAC ACGGCGGG(PSU)G CUAACGUCCG UCGUGAAGAG GGAAACAACC CAGACCGCCA GCUAAGGUCC CAAAGUCAUG GUUAAGUGGG AAACGAUGUG GGAAGGCCCA GACAGCCAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAAAGCGUAA UAGCUCACUG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUCUGUAAG CCUGCGAAGG UGUGCUGUGA GGCAUGCUGG AGGUAUCAGA AGUGCGAAUG CUGACAUAAG UAACGAUAAA GCGGGUGAAA AGCCCGCUCG CCGGAAGACC AAGGGUUCCU GUCCAACGUU AAUCGGGGCA GGGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGAAGG CUAUGUUGGC CGGGCGACGG UUGUCCCGGU UUAAGCGUGU AGGCUGGUUU UCCAGGCAAA UCCGGAAAAU CAAGGCUGAG GCGUGAUGAC GAGGCACUAC GGUGCUGAAG CAACAAAUGC CCUGCUUCCA GGAAAAGCCU CUAAGCAUCA GGUAACAUCA AAUCGUACCC CAAACCGACA C(6MZ)GGUGGUCA GGUAGAGAAU ACCAAGGCGC UUGAGAGAAC UCGGGUGAAG GAACUAGGCA AAAUGGUGCC GUAACUUCGG GAGAAGGCAC GCUGAUAUGU AGGUGAGGUC CCUCGCGGAU GGAGCUGAAA UCAGUCGAAG AUACCAGCUG GCUGCAACUG UUUAUUAAAA ACACAGCACU GUGCAAACAC GAAAGUGGAC GUAUACGGUG UGACGCCU(2MG)C CCGGUGCCGG AAGGUUAAUU GAUGGGGUUA GCGCAAGCGA AGCUCUUGAU CGAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGAC(5MC)UGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGAC UCAGUGAAAU UGAACUCGCU GUG(6MZ)AGAUGC AGUGUACCCG CGGCAAGACG GAAAGACCCC GU(G7M)AACCUUU ACUAUAGCUU GACACUGAAC AUUGAGCCUU GAUGUGUAGG AUAGGUGGGA GGCUUUGAAG UGUGGACGCC AGUCUGCAUG GAGCCGACCU UGAAAUACCA CCCUUUAAUG UUUGAUGUUC UAACGUUGAC CCGUAAUCCG GGUUGCGGAC AGUGUCUGGU GGGUAGUUUG ACUG(OMG)GGCGG UCUCCUCCUA AAGAGUAACG GAGGAGCACG AAGGUUGGCU AAUCCUGGUC GGACAUCAGG AGGUUAGUGC AAUGGCAUAA GCCAGCUUGA CUGCGAGCGU GACGGCGCGA GCAGGUGCGA AAGCAGGUCA UAGUGAUCCG GUGGUUCUGA AUGGAAGGGC CAUCGCUCAA CGGAUAAAAG GUACUCCG(2MG)G GAUAACAGGC (PSU)GAUACCGCC CAAGAGUUCA UAUCGACGGC GGUGUUUGGC A(OMC)CUCG(2MA)(PSU)GU CGGCUCAUCA CAUCCUGGGG CUGAAGUAGG UCCCAAGGGU AUGGC(OMU)GUUC GCCAUUUAAA GUGGUACGCG AGC(PSU)GGGUUU AGAACGUCGU GAGACAG(PSU)(PSU)C GGUCCCUAUC UGCCGUGGGC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACUGCC CGGUAGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAAGGGUCC UGAAGGAACG UUGAAGACGA CGACGUUGAU AGGCCGGGUG UGUAAGCGCA GCGAUGCGUU GAGCUAACCG GUACUAAUGA ACCGUGAGGC UUAACCU
MassTheoretical: 939.60725 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #5: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCAU
MassTheoretical: 38.79009 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #6: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #7: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.291562 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #8: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #9: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #10: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #11: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #12: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #13: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #14: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #15: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.327261 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #16: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.505746 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #17: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #18: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #19: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #20: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #21: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #22: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #23: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.078874 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #24: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #25: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.275498 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #26: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #27: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.155267 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #28: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #29: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #30: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.928 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #31: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #32: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #33: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #34: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #35: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCCGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCCGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCC(G7M)CGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUC
MassTheoretical: 497.07475 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #36: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.971764 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #37: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #38: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #39: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.361878 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #40: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.326251 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #41: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #42: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #43: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #44: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.325117 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #45: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.4872 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #46: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.683053 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #47: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #48: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.546442 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #49: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #50: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #51: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #52: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.466477 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #53: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.323902 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #54: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.577268 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #55: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.629744 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #56: protein, ermC Nacent chain

ProteinName: ermC Nacent chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.895097 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #57: nucleic-acid, P-site Isoleucine tRNA (77-MER)

nucleic acidName: P-site Isoleucine tRNA (77-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGGCUUAUAG CUCAGGUGGU UAGAGCGCAC CCCUGAUAAG GGUGAGGUCG GUGGUUCAAG UCCACUCAGG CCUACCA
MassTheoretical: 24.839754 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #58: nucleic-acid, atRNA synthetic Stop tRNA (76-MER)

nucleic acidName: atRNA synthetic Stop tRNA (76-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGGUGGUGG CUCAGAAGGG AGAGCAGCGG CCUUCAGAGC CGCGAGACGG GGGUUCGAUU CCCCUCCGCU CCACCA
MassTheoretical: 24.632693 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #59: nucleic-acid, E-site val tRNA (76-MER)

nucleic acidName: E-site val tRNA (76-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGUGAUUAG CUCAGCUGGG AGAGCACCUC CCUUACAAGG AGGUGGUCGG CGGUUCGAUC CCGUCAUCAC CCACCA
MassTheoretical: 24.444531 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #60: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAAUCUGAA C
MassTheoretical: 3.491138 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

+
Component #61: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 359 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #62: ligand, ERYTHROMYCIN A

LigandName: ERYTHROMYCIN AErythromycin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.733927 kDa

+
Component #63: ligand, 2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxi...

LigandName: 2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.305374 kDa

+
Component #64: ligand, water

LigandName: water / Number of Copies: 854 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: OTHER / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 1 e/Å2 / Illumination Mode: SPOT SCAN
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 600

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 45000
3D reconstructionSoftware: RELION / Resolution: 2.9 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more