[English] 日本語
Yorodumi
- EMDB-22345: 70S ribosome Flavobacterium johnsoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22345
Title70S ribosome Flavobacterium johnsoniae
Map data
Sample70S ribosome Flavobacterium johnsoniae:
(nucleic-acidNucleic acid) x 3 / (50S ribosomal protein ...) x 30 / (30S ribosomal protein ...) x 20 / (ligand) x 2
Function / homology
Function and homology information


large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding
30S ribosomal protein S17 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein L25, C-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, beta domain ...30S ribosomal protein S17 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein L25, C-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, beta domain / Ribosomal protein S3, conserved site / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L6, bacterial-type / Ribosomal protein S14, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L2, domain 3 / Ribosomal protein L23/L15e core domain superfamily / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / K homology domain-like, alpha/beta / Ribosomal protein S10, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Nucleic acid-binding, OB-fold / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L35 / Ribosomal protein S19/S15, superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein S4/S9 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Protein of unknown function DUF4295 / Ribosomal protein L28/L24 / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / L28p-like / Nucleotide-binding alpha-beta plait domain superfamily / Zinc-binding ribosomal protein / RNA-binding S4 domain superfamily / Ribosomal protein S3, C-terminal / Ribosomal protein L6 / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein L25, long-form / Ribosomal protein L22/L17 / Ribosomal protein L15, conserved site / Ribosomal protein S14 / Ribosomal protein L28 / Ribosomal protein L3 / Ribosomal protein S18 / Ribosomal protein L27 / Ribosomal protein L33 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L21 / Ribosomal protein S10
30S ribosomal protein S8 / 30S ribosomal protein S7 / 30S ribosomal protein S19 / 30S ribosomal protein S17 / 50S ribosomal protein L31 / 50S ribosomal protein L6 / 50S ribosomal protein L30 / 50S ribosomal protein L17 / 50S ribosomal protein L9 / 50S ribosomal protein L3 ...30S ribosomal protein S8 / 30S ribosomal protein S7 / 30S ribosomal protein S19 / 30S ribosomal protein S17 / 50S ribosomal protein L31 / 50S ribosomal protein L6 / 50S ribosomal protein L30 / 50S ribosomal protein L17 / 50S ribosomal protein L9 / 50S ribosomal protein L3 / 50S ribosomal protein L27 / 50S ribosomal protein L19 / 30S ribosomal protein S16 / 30S ribosomal protein S15 / 50S ribosomal protein L25 / 30S ribosomal protein S9 / 50S ribosomal protein L4 / 50S ribosomal protein L15 / 50S ribosomal protein L18 / 50S ribosomal protein L36 / Uncharacterized protein / 50S ribosomal protein L14 / Uncharacterized protein / 30S ribosomal protein S3 / 50S ribosomal protein L21 / 50S ribosomal protein L34 / 30S ribosomal protein S12 / 50S ribosomal protein L32 / 50S ribosomal protein L22 / 50S ribosomal protein L24 / 50S ribosomal protein L16 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 50S ribosomal protein L2 / 30S ribosomal protein S14 / 50S ribosomal protein L20 / 50S ribosomal protein L13 / 50S ribosomal protein L28 / 30S ribosomal protein S20 / 50S ribosomal protein L33 / 30S ribosomal protein S18 / 30S ribosomal protein S6 / 50S ribosomal protein L23 / 50S ribosomal protein L35 / 30S ribosomal protein S11 / 30S ribosomal protein S21 / 30S ribosomal protein S10 / 50S ribosomal protein L29
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsOrtega J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2019-05799 Canada
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.
Authors: Vikash Jha / Bappaditya Roy / Dushyant Jahagirdar / Zakkary A McNutt / Elan A Shatoff / Bethany L Boleratz / Dean E Watkins / Ralf Bundschuh / Kaustuv Basu / Joaquin Ortega / Kurt Fredrick /
Abstract: Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the ...Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein-bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 23, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jil
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_22345.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 360 pix.
= 386.28 Å
1.07 Å/pix.
x 360 pix.
= 386.28 Å
1.07 Å/pix.
x 360 pix.
= 386.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-15.121298 - 26.298506
Average (Standard dev.)-2.4915562e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z386.280386.280386.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-15.12126.299-0.000

-
Supplemental data

-
Sample components

+
Entire 70S ribosome Flavobacterium johnsoniae

EntireName: 70S ribosome Flavobacterium johnsoniae / Number of components: 56

+
Component #1: protein, 70S ribosome Flavobacterium johnsoniae

ProteinName: 70S ribosome Flavobacterium johnsoniae / Recombinant expression: No
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #2: nucleic-acid, RNA (2862-MER)

nucleic acidName: RNA (2862-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: CAACGAGGGC GUAUGGGGAA UGCCUAGGCU CUCAGAGGCG AUGAAGGACG UGAUAAGCUG CGAAAAGCUG CGGGGACUGG CACACACAGA UUGAUCCGCA GAUAUCCGAA UGGGGCAACC CGCUAUAUUG AAGAUAUAGC ACACCGAUAG GUGGGCAAAC CCGCUGAACU ...Sequence:
CAACGAGGGC GUAUGGGGAA UGCCUAGGCU CUCAGAGGCG AUGAAGGACG UGAUAAGCUG CGAAAAGCUG CGGGGACUGG CACACACAGA UUGAUCCGCA GAUAUCCGAA UGGGGCAACC CGCUAUAUUG AAGAUAUAGC ACACCGAUAG GUGGGCAAAC CCGCUGAACU GAAACAUCUA AGUAGGCGGA GGAGAAGAAA ACAAAAGUGA UUCCGUAAGU AGUGGCGAGC GAACGCGGAU UAGCCCAAAC CAGUGCUGUU ACGGCAGUGC UGGGGUUGUA GGACCACGAC AUUUUAUGCA UGCAGAACCG GAAGUUACUG GAAAGUGACG CCAAAGAGGG UGAUAGCCCC GUAUGGGUAA UAAAUGUAAU AGAUAGUGGU AUCCUGAGUA GGGCGGGACA CGUGAAACCC UGUCUGAAUU CGGCGGGACC AUCCGCUAAG GCUAAAUACU CCUGAGAGAC CGAUAGUGAA CCAGUACCGU GAGGGAAAGG UGAAAAGAAC CGUGAAUAAC GGAGUGAAAU AGAUCCUGAA ACCAUACGCU UACAAGCGGU CGGAGCCCUU UCGUGGGGUG ACGGCGUGCC UUUUGCAUAA UGAGCCUACG AGUUAACGCU GCUGGCAAGG AUAAGUACUU CAGGUACGGA UCCGCAGCGA AAGCGAGUCU GAAUAGGGCG CUUUAGUCAG UAGUGUUAGA CGCGAAACCG UGUGAUCUAC CCAUGGGCAG GUUGAAGCUG UGGUAACACA CAGUGGAGGA CCGAACCGGU UGACGUUGAA AAGUCUUCGG AUGACCUGUG GGUAGGGGUG AAAGGCCAAU CAAACUCGGA AAUAGCUCGU ACUCCCCGAA AUGCAUUUAG GUGCAGCGUU AGUUAUAAAG UUAUACAGAG GUAGAGCUAC UGAUUGGAUG CGGGGGCUUC ACCGCCCACC AAUUCCUGAC AAACUCCGAA UGCUGUAUAA UGUUCACUAA CAGUGAGGGC UUGGGUGCUA AGGUCCAAGU CCGAGAGGGA AAGAACCCAG ACCAUCAGCU AAGGUCCCCA AAUAUAUGCU AAGUUGAAAG AACGAGGUUU GUCUGCCCAG ACAGCUAGGA UGUUGGCUUG GAAGCAGCCA UUCAUUUAAA GAGUGCGUAA CAGCUCACUA GUCGAGCGGA CGAGCAUGGA UAAUAAUCGG GCAUAAGCAU AUUACCGAAG CUAUGGAUUU GCAAGUAAUU GCAAGUGGUA GGGGAGCAUU CUAACAGGGU UGAAGGUUUU UCGUAAGGAG GGCUGGACUG GUUAGAAAAG AAAAUGUAGG CAUAAGUAAC GAUAAUGCGG GCGAGAAACC CGCACACCGA AAAACUAAGG UUUCCACAGC UAUGCUAAUC AGCUGUGGGU UAGUCUGGUC CUAAGGCGAA CCCGAAAGGG ACAGUCGAUG GCUAACGGGU UAAUAUUCCC GUACUACUAA UUACUGUGAU GGGGUGACGG AGUGAUGAAA GCGCCGCGAA CUGACGGAAU AGUUCGUUGA AGUACCUAGC UAUAGGUCCU GUAGUAAAAU GCGCAGGAAC UGGUGAAAUA CGAUAGUACU CGGAGUCUUC GGACAAAGAG AUAGUGCGCC UAAGGGCUUC CAAGAAAAAC CUCUAAACUU CAGGUAAUUA GUACCAGUAC CGUAAACCGA CACAGGUAGU UGAGGAGAGA AUCCUAAGGU GCUCGAGAUA UUCAUGGCUA AGGAAUUAGG CAAAAUAGAC CUGUAACUUC GGGAGAAAGG UCGCCCUGAG CAAUCAGGGC CGCAGUGAAG AGGUCCAGGC GACUGUUUAU CAAAAACACA GGGCUCUGCA AAAUCGUAAG AUGAAGUAUA GGGCCUGACA CCUGCCCGGU GCUGGAAGGU UAAGAGGAGA UGUUAUCUUC GGAGAAGCAU UGAAUUGAAG CCCCAGUAAA CGGCGGCCGU AACUAUAACG GUCCUAAGGU AGCGAAAUUC CUUGUCGGGU AAGUUCCGAC CUGCACGAAU GGUGUAACGA UCUGGACACU GUCUCAGCCA UGAGCUCGGU GAAAUUGUAG UAACGGUGAA GAUGCCGUUU ACCCGCAGUG GGACGAAAAG ACCCUGUGCA CCUUUACUAU AGCUUAGUAC UGACCUUGGA UAAAUGAUGU GUAGGAUAGG UUGGAGACUA UGAAGCGGCG UCGCCAGGCG UUGUGGAGUC AUUGUUGAAA UACAACCCUU UGUUUAUCUG AGGCCUAACC UCGCUAUGCG GGGGACAGUG CUUGGUGGGU AGUUUGACUG GGGUGGUCGC CUCCAAAAGA GUAACGGAGG CUUCUAAAGG UUCCCUCAGU ACGCUUGGUA ACCGUGCGUA GAGUGCAAUG GCAUAAGGGA GCUUGACUGA GAGACAUACA GGUCGAUCAG GUACGAAAGU AGAGCAUAGU GAUCCGGUGG UUCCGCAUGG AAGGGCCAUC GCUCAAAGGA UAAAAGGUAC GCCGGGGAUA ACAGGCUGAU CUCCCCCAAG AGUUCAUAUC GACGGGGGGG UUUGGCACCU CGAUGUCGGC UCGUCACAUC CUGGGGCUGG AGAAGGUCCC AAGGGUUGGG CUGUUCGCCC AUUAAAGUGG UACGCGAGCU GGGUUCAGAA CGUCGUGAGA CAGUUCGGUC UCUAUCUACU GCGGGCGUUA GAAAUUUGAG UGGAUCUGAU UCUAGUACGA GAGGACCGAA UUGGACUAAC CUCUAGUGUA UCUGUUGUCC CGCCAGGGGC ACCGCAGAGU AGCUACGUUG GGAAGGGAUA AGCGCUGAAA GCAUAUAAGC GCGAAACCCA CCACAAGAUG AGAUUUCUUU UAAGGAUCGU GGAAGAUGAC CACGUUGAUA GGCUAUAGAU GUAAAGGCAG UAAUGUCAUA GUCGAGUAGU ACUAAUAAUC CG
MassTheoretical: 927.288188 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #3: nucleic-acid, RNA (1519-MER)

nucleic acidName: RNA (1519-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAUACGAUGA AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC UUAACACAUG CAAGUCGAGG GGUAGAAGUC UUCGGGCUUU GAGACCGGCG CACGGGUGCG UAACGCGUAU GCAAUCUGCC UUUCACAGAG GGAUAGCCCA GAGAAAUUUG GAUUAAUACC ...Sequence:
UAUACGAUGA AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC UUAACACAUG CAAGUCGAGG GGUAGAAGUC UUCGGGCUUU GAGACCGGCG CACGGGUGCG UAACGCGUAU GCAAUCUGCC UUUCACAGAG GGAUAGCCCA GAGAAAUUUG GAUUAAUACC UCAUAGUAUU AUAGAGCGGC AUCACUUUAU AAUUAAAGUC ACAACGGUGA AAGAUGAGCA UGCGUCCCAU UAGCUAGUUG GUAAGGUAAC GGCUUACCAA GGCCACGAUG GGUAGGGGUC CUGAGAGGGA GAUCCCCCAC ACUGGUACUG AGACACGGAC CAGACUCCUA CGGGAGGCAG CAGUGAGGAA UAUUGGUCAA UGGACGCAAG UCUGAACCAG CCAUGCCGCG UGCAGGAUGA CGGUCCUAUG GAUUGUAAAC UGCUUUUGUA CGAGAAGAAA CACUCCUAUA UAUAGGAGCU UGACGGUAUC GUAAGAAUAA GGAUCGGCUA ACUCCGUGCC AGCAGCCGCG GUAAUACGGA GGAUCCAAGC GUUAUCCGGA AUCACUGGGU UUAAAGGGUC CGUAGGCGGU UUAGUAAGUC AGUGGUGAAA GCCCAUCGCU CAACGGUGGA ACGGCCAUUG AUACUGCUGA ACUUGAAUUA CUGGGAAGUA ACUAGAAUAU GUAGUGUAGC GGUGAAAUGC UUAGAUAUUA CAUGGAAUAC CAAUUGCGAA GGCAGGUUAC UACCAGUUUA UUGACGCUGA UGGACGAAAG CGUGGGGAGC GAACAGGAUU AGAUACCCUG GUAGUCCACG CCGUAAACGA UGGAUACUAG CUGUUGGGCG CAAGUUCAGU GGCUAAGCGA AAGUGAUAAG UAUCCCACCU GGGGAGUACG AACGCAAGUU UGAAACUCAA AGGAAUUGAC GGGGGCCCGC ACAAGCGGUG GAACAUGUGG UUUAAUUCGA UGAUACGCGA GGAACCUUAC CAAGGCUUAA AUGCAGACUG ACCGAUUUGG AAACAGAUCU UAUCGCAAGA CAGUUUACAA GGUGCUGCAU GGUUGUCGUC AGCUCGUGCC GUGAGGUGUC AGGUUAAGUC CUAUAACGAG CGCAACCCCU GUUGUUAGUU GCCAGCGAGU GAUGUCGGGA ACUCUAACAA GACUGCCAGU GCAAACUGUG AGGAAGGUGG GGAUGACGUC AAAUCAUCAC GGCCCUUACG CCUUGGGCUA CACACGUGCU ACAAUGGCCG GUACAGAGAG CAGCCACUGG GUGACCAGGA GCGAAUCUAU AAAGCCGGUC ACAGUUCGGA UCGGAGUCUG CAACUCGACU CCGUGAAGCU GGAAUCGCUA GUAAUCGGAU AUCAGCCAUG AUCCGGUGAA UACGUUCCCG GGCCUUGUAC ACACCGCCCG UCAAGCCAUG GAAGCUGGGG GUGCCUGAAG UCGGUGACCG CAAGGAGCUG CCUAGGGUAA AACUGGUAAC UAGGGCUAAG UCGUAACAAG GUAGCCGUAC CGGAAGGUGC GGCUGGAACA CCUCCUUUCU
MassTheoretical: 491.83325 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #4: nucleic-acid, RNA (111-MER)

nucleic acidName: RNA (111-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUAAGGUGGU UAUUGCGGCG GGGCUCACCU CUUCCCAUCC CGAACAGAGA AGUUAAGCCC GCUUGCGCAG AUGGUACUGC AGUUUUGUGG GAGAGUAUGU CGUCGCCUUU C
MassTheoretical: 35.661992 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #5: protein, 50S ribosomal protein L38

ProteinName: 50S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.569749 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #6: protein, 30S ribosomal protein S22

ProteinName: 30S ribosomal protein S22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.696608 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #7: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.991619 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #8: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.975359 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #9: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.187557 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #10: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.79932 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #11: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.420445 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #12: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.968622 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #13: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.578273 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #14: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.339537 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #15: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.994265 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #16: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.075122 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #17: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.092869 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #18: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.66072 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #19: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.316622 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #20: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.244699 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #21: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.90152 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #22: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.475993 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #23: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.690438 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #24: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.439517 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #25: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.89165 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #26: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.422824 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #27: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.942626 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #28: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.189451 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #29: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.643993 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #30: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.646128 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #31: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.518691 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #32: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.935232 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #33: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.324544 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #34: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.522242 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #35: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.557577 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #36: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.886365 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #37: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.950443 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #38: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.20602 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #39: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.376448 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #40: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.493707 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #41: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.652163 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #42: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.464888 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #43: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.44664 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #44: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.700957 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #45: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.121425 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #46: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.734152 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #47: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.211011 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #48: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.565339 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #49: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.106588 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #50: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.1089 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #51: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.378475 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #52: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.278883 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #53: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.442211 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #54: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.433809 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

+
Component #55: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 325 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #56: ligand, water

LigandName: water / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 50 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 / Number of projections: 705543
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
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