[English] 日本語
Yorodumi
- EMDB-4638: Structure of a bacterial 50S ribosomal subunit in complex with th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4638
TitleStructure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid
Map data
SampleStructure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid:
(nucleic-acidNucleic acid) x 3 / (50S ribosomal protein ...) x 28 / (ligand) x 5
Function / homology
Function and homology information


endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / ribosome assembly / DNA-templated transcription, termination ...endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / ribosome assembly / DNA-templated transcription, termination / response to reactive oxygen species / regulation of cell growth / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / response to radiation / 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 / cytosol
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L9 signature. ...Ribosomal protein L25, short-form / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / 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 L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal L25p family / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L19 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L27 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L20 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-type / Ribosomal L28 family / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L16 / Ribosomal protein L30, bacterial-type / Ribosomal L32p protein family / Ribosomal L27 protein / Ribosomal protein L27 / Ribosomal protein L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L32p / L21-like superfamily / Ribosomal protein L21-like / Ribosomal prokaryotic L21 protein / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L13, bacterial-type / Ribosomal protein L24 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L23/L25, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L5 / Ribosomal protein L5, N-terminal / Ribosomal protein L15 signature.
Similarity search - Domain/homology
50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L16 / 50S ribosomal protein L4 ...50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L16 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L23 / 50S ribosomal protein L36 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / 50S ribosomal protein L35 / 50S ribosomal protein L34 / 50S ribosomal protein L33 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 50S ribosomal protein L28 / 50S ribosomal protein L27 / 50S ribosomal protein L20 / 50S ribosomal protein L19 / 50S ribosomal protein L15 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsScaiola A / Leibundgut M / Boehringer D / Ritz D
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic.
Authors: Alain Scaiola / Marc Leibundgut / Daniel Boehringer / Patrick Caspers / Daniel Bur / Hans H Locher / Georg Rueedi / Daniel Ritz /
Abstract: Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl ...Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with the peptidyl transferase reaction. Cadazolid is the first member of quinoxolidinone antibiotics, which are characterized by combining the pharmacophores of oxazolidinones and fluoroquinolones, and it is evaluated for treatment of Clostridium difficile gastrointestinal infections that frequently occur in hospitalized patients. In vitro protein synthesis inhibition by cadazolid was shown in Escherichia coli and Staphylococcus aureus, including an isolate resistant against linezolid, the prototypical oxazolidinone antibiotic. To better understand the mechanism of inhibition, we determined a 3.0 Å cryo-electron microscopy structure of cadazolid bound to the E. coli ribosome in complex with mRNA and initiator tRNA. Here we show that cadazolid binds with its oxazolidinone moiety in a binding pocket in close vicinity of the PTC as observed previously for linezolid, and that it extends its unique fluoroquinolone moiety towards the A-site of the PTC. In this position, the drug inhibits protein synthesis by interfering with the binding of tRNA to the A-site, suggesting that its chemical features also can enable the inhibition of linezolid-resistant strains.
History
DepositionFeb 27, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qul
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4638.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.12 Å
1.08 Å/pix.
x 290 pix.
= 312.91 Å
1.08 Å/pix.
x 290 pix.
= 312.91 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.079 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.08
Minimum - Maximum-0.38431114 - 0.6159274
Average (Standard dev.)0.0015044372 (±0.025905425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290280
Spacing290290280
CellA: 312.91 Å / B: 312.91 Å / C: 302.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0791.0791.079
M x/y/z290290280
origin x/y/z0.0000.0000.000
length x/y/z312.910312.910302.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290280
D min/max/mean-0.3840.6160.002

-
Supplemental data

-
Segmentation: #1

Fileemd_4638_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_4638_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_4638_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Structure of a bacterial 50S ribosomal subunit in complex with th...

EntireName: Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid
Number of components: 37

+
Component #1: protein, Structure of a bacterial 50S ribosomal subunit in comple...

ProteinName: Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

+
Component #2: nucleic-acid, P-site fMet-tRNA(fMet)

nucleic acidName: P-site fMet-tRNA(fMet) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACCA
MassTheoretical: 1.223818 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #3: 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 ACGCUGGCGU GUGACUGCGU ACCUUUUGUA UAAUGGGUCA GCGACUUAUA UUCUGUAGCA AGGUUAACCG AAUAGGGGAG CCGAAGGGAA ACCGAGUCUU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACUAA CUGGAGGACC GAACCGACUA AUGUUGAAAA AUUAGCGGAU GACUUGUGGC UGGGGGUGAA AGGCCAAUCA AACCGGGAGA UAGCUGGUUC UCCCCGAAAG CUAUUUAGGU AGCGCCUCGU GAAUUCAUCU CCGGGGGUAG AGCACUGUUU CGGCAAGGGG GCUUACCAAC CCGAUGCAAA CUGCGAAUAC CGGAGAAUGU UAUCACGGGA GACACACGGC GGGUGCUAAC GUCCGUCGUG AAGAGGGAAA CAACCCAGAC CGCCAGCUAA GGUCCCAAAG UCAUGGUUAA GUGGGAAACG AUGUGGGAAG GCCCAGACAG CCAGGAUGUU GGCUUAGAAG CAGCCAUCAU UUAAAGAAAG CGUAAUAGCU CACUGGUCGA GUCGGCCUGC GCGGAAGAUG UAACGGGGCU AAACCAUGCA CCGAAGCUGC GGCAGCGACG CUGCGUUGUU GGGUAGGGGA GCGUUCUGUA AGCCUGCGAA GGUGUGCUGU GAGGCAUGCU GGAGGUAUCA GAAGUGCGAA UGCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAGGCCG AAAGGCGUAG UCGAUGGGAA ACAGGUUAAU AUUCCUGUAC UUGGUGUUAC UGCGAAGGGG GGACGGAGAA GGCUAUGUUG GCCGGGCGAC GGUUGUCCCG GUUUAAGCGU GUAGGCUGGU UUUCCAGGCA AAUCCGGAAA AUCAAGGCUG AGGCGUGAUG ACGAGGCGCU GAAGCAACAA AUGCCCUGCU UCCAGGAAAA GCCUCUAAGC AUCAGGUAAC AUCAAAUCGU ACCCCAAACC GACACAGGUG GUCAGGUAGA GAAUACCAAG GCGCUUGAGA GAACUCGGGU GAAGGAACUA GGCAAAAUGG UGCCGUAACU UCGGGAGAAG GCACGCUGAU AUGUAGGUGA GGUCCCUCGC GGAUGGAGCU GAAAUCAGUC GAAGAUACCA GCUGGCUGCA ACUGUUUAUU AAAAACACAG CACUGUGCAA ACACGAAAGU GGACGUAUAC GGUGUGACGC CUGCCCGGUG CCGGAAGGUU AAUUGAUGGG GUUAGCGCAA GCGAAGCUCU UGAUCGAAGC CCCGGUAAAC GGCGGCCGUA ACUAUAACGG UCCUAAGGUA GCGAAAUUCC UUGUCGGGUA AGUUCCGACC UGCACGAAUG GCGUAAUGAU GGCCAGGCUG UCUCCACCCG AGACUCAGUG AAAUUGAACU CGCUGUGAAG AUGCAGUGUA CCCGCGGCAA GACGGAAAGA CCCCGUGAAC CUUUACUAUA GCUUGACACU GAACAUUGAU UGAUGUUCUA ACGUUGACCC GUAAUCCGGG UUGCGGACAG UGUCUGGUGG GUAGUUUGAC UGGGGCGGUC UCCUCCUAAA GAGUAACGGA GGAGCACGAA GGUUGGCUAA UCCUGGUCGG ACAUCAGGAG GUUAGUGCAA UGGCAUAAGC CAGCUUGACU GCGAGCGUGA CGGCGCGAGC AGGUGCGAAA GCAGGUCAUA GUGAUCCGGU GGUUCUGAAU GGAAGGGCCA UCGCUCAACG GAUAAAAGGU ACUCCGGGGA UAACAGGCUG AUACCGCCCA AGAGUUCAUA UCGACGGCGG UGUUUGGCAC CUCGAUGUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGCUGUUCGC CAUUUAAAGU GGUACGCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AGGGGGGCUG CUCCUAGUAC GAGAGGACCG GAGUGGACGC AUCACUGGUG UUCGGGUUGU CAUGCCAAUG GCACUGCCCG GUAGCUAAAU GCGGAAGAGA UAAGUGCUGA AAGCAUCUAA GCACGAAACU UGCCCCGAGA UGAGUUCUCC CUGACCCUUU AAGGGUCCUG AAGGAACGUU GAAGACGACG ACGUUGAUAG GCCGGGUGUG UAAGCGCAGC GAUGCGUUGA GCUAACCGGU ACUAAUGAAC CGUGAGGCUU AACCU
MassTheoretical: 906.514125 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #4: 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 (E. coli)

+
Component #5: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #6: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #7: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #8: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #9: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #10: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #11: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #12: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #13: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #14: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #15: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #16: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #17: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #18: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #19: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #20: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #21: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #22: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #23: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #24: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #25: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #26: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #27: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #28: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #29: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #30: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #31: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #32: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #33: ligand, N-FORMYLMETHIONINE

LigandName: N-FORMYLMETHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.177221 kDa

+
Component #34: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 382 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #35: ligand, ADENOSINE-5'-MONOPHOSPHATE

LigandName: ADENOSINE-5'-MONOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.347221 kDa

+
Component #36: ligand, cadazolid

LigandName: cadazolid / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.585553 kDa

+
Component #37: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.14 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 59148
3D reconstructionSoftware: RELION / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Read more

-
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.

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