[English] 日本語
Yorodumi
- EMDB-71035: Flavobacterium johnsoniae 30S ribosomal subunit, ZAM64 mutant. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71035
TitleFlavobacterium johnsoniae 30S ribosomal subunit, ZAM64 mutant.
Map data
Sample
  • Complex: Ribosome
    • RNA: x 1 types
    • Protein or peptide: x 18 types
KeywordsRibosome / 30S
Function / homology
Function and homology information


ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome ...ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / : / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / K homology domain-like, alpha/beta / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e / S4 RNA-binding domain / Ribosomal S11, conserved site / S4 domain / Ribosomal protein S11 signature. / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 ...Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsOrtega J / Arpin D
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of a specialized 70S initiation complex.
Authors: Dominic Arpin / Bappaditya Roy / Fawwaz M Naeem / Kurt Fredrick / Joaquin Ortega /
Abstract: Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes ...Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.
History
DepositionJun 4, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71035.png

Downloads & links

-
Map

FileDownload / File: emd_71035.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.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08801278 - 0.3456893
Average (Standard dev.)0.00038415883 (±0.01160135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_71035_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71035_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71035_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Ribosome

EntireName: Ribosome
Components
  • Complex: Ribosome
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20

+
Supramolecule #1: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)

+
Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 491.83325 KDa
SequenceString: UAUACGAUGA AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC UUAACACAUG CAAGUCGAGG GGUAGAAGUC UUCGGGCUU UGAGACCGGC GCACGGGUGC GUAACGCGUA UGCAAUCUGC CUUUCACAGA GGGAUAGCCC AGAGAAAUUU G GAUUAAUA ...String:
UAUACGAUGA AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC UUAACACAUG CAAGUCGAGG GGUAGAAGUC UUCGGGCUU UGAGACCGGC GCACGGGUGC GUAACGCGUA UGCAAUCUGC CUUUCACAGA GGGAUAGCCC AGAGAAAUUU G GAUUAAUA CCUCAUAGUA UUAUAGAGCG GCAUCACUUU AUAAUUAAAG UCACAACGGU GAAAGAUGAG CAUGCGUCCC AU UAGCUAG UUGGUAAGGU AACGGCUUAC CAAGGCCACG AUGGGUAGGG GUCCUGAGAG GGAGAUCCCC CACACUGGUA CUG AGACAC GGACCAGACU CCUACGGGAG GCAGCAGUGA GGAAUAUUGG UCAAUGGACG CAAGUCUGAA CCAGCCAUGC CGCG UGCAG GAUGACGGUC CUAUGGAUUG UAAACUGCUU UUGUACGAGA AGAAACACUC CUAUAUAUAG GAGCUUGACG GUAUC GUAA GAAUAAGGAU CGGCUAACUC CGUGCCAGCA GCCGCGGUAA UACGGAGGAU CCAAGCGUUA UCCGGAAUCA CUGGGU UUA AAGGGUCCGU AGGCGGUUUA GUAAGUCAGU GGUGAAAGCC CAUCGCUCAA CGGUGGAACG GCCAUUGAUA CUGCUGA AC UUGAAUUACU GGGAAGUAAC UAGAAUAUGU AGUGUAGCGG UGAAAUGCUU AGAUAUUACA UGGAAUACCA AUUGCGAA G GCAGGUUACU ACCAGUUUAU UGACGCUGAU GGACGAAAGC GUGGGGAGCG AACAGGAUUA GAUACCCUGG UAGUCCACG CCGUAAACGA UGGAUACUAG CUGUUGGGCG CAAGUUCAGU GGCUAAGCGA AAGUGAUAAG UAUCCCACCU GGGGAGUACG AACGCAAGU UUGAAACUCA AAGGAAUUGA CGGGGGCCCG CACAAGCGGU GGAACAUGUG GUUUAAUUCG AUGAUACGCG A GGAACCUU ACCAAGGCUU AAAUGCAGAC UGACCGAUUU GGAAACAGAU CUUAUCGCAA GACAGUUUAC AAGGUGCUGC AU GGUUGUC GUCAGCUCGU GCCGUGAGGU GUCAGGUUAA GUCCUAUAAC GAGCGCAACC CCUGUUGUUA GUUGCCAGCG AGU GAUGUC GGGAACUCUA ACAAGACUGC CAGUGCAAAC UGUGAGGAAG GUGGGGAUGA CGUCAAAUCA UCACGGCCCU UACG CCUUG GGCUACACAC GUGCUACAAU GGCCGGUACA GAGAGCAGCC ACUGGGUGAC CAGGAGCGAA UCUAUAAAGC CGGUC ACAG UUCGGAUCGG AGUCUGCAAC UCGACUCCGU GAAGCUGGAA UCGCUAGUAA UCGGAUAUCA GCCAUGAUCC GGUGAA UAC GUUCCCGGGC CUUGUACACA CCGCCCGUCA AGCCAUGGAA GCUGGGGGUG CCUGAAGUCG GUGACCGCAA GGAGCUG CC UAGGGUAAAA CUGGUAACUA GGGCUAAGUC GUAACAAGGU AGCCGUACCG GAAGGUGCGG CUGGAACACC UCCUUUCU

+
Macromolecule #2: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 27.886365 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString: MGQKTNPIGN RLGIIRGWDS NWYGGNDYGD KLAEDHKIRK YIHARLSKAS VSKVIIERTL KLVTVTITTA RPGIIIGKGG QEVDKLKEE LKKVTDKEVQ INIFEIKRPE LDAYLVATSI ARQIESRISY RRAIKMAIAA SMRMNAEGIK VLISGRLNGA E MARSEGFK ...String:
MGQKTNPIGN RLGIIRGWDS NWYGGNDYGD KLAEDHKIRK YIHARLSKAS VSKVIIERTL KLVTVTITTA RPGIIIGKGG QEVDKLKEE LKKVTDKEVQ INIFEIKRPE LDAYLVATSI ARQIESRISY RRAIKMAIAA SMRMNAEGIK VLISGRLNGA E MARSEGFK EGRIPLSTFR ADIDYALAEA HTTYGRMGIK VWIMKGEVYG KRDLSPLAGM DKKQSGTGGG KGGDAPRGKS NF NKGGKPD ARKRK

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #3: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 22.950443 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString: MARYTGPKTK IARKFGEAIF GDDKSFEKRN YPPGQHGMAK KRGKKSEYAV QLMEKQKAKY SYGILEKQFR NLFEKASATK GVTGEVLLQ LCEARLDNVV FRMGIAPSRR GARQIVSHRH ITVNGEVVNI PSYHLKPGDK VAVREKSKSL EAIERSLSNS S HVYEWITW ...String:
MARYTGPKTK IARKFGEAIF GDDKSFEKRN YPPGQHGMAK KRGKKSEYAV QLMEKQKAKY SYGILEKQFR NLFEKASATK GVTGEVLLQ LCEARLDNVV FRMGIAPSRR GARQIVSHRH ITVNGEVVNI PSYHLKPGDK VAVREKSKSL EAIERSLSNS S HVYEWITW NNDLKEGTFV SVPARLQIPE NIKEQLIVEL YNK

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #4: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 18.20602 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MSKYKNVELV KPSGLELKDR LVSVNRVTKV TKGGRAFGFS AIVVVGDENG VVGHGLGKSK DVSEAIAKAV EDAKKNLVRI PLNGQSVPH EQKGKFGGAR VFLIPASHGT GVIAGGAVRS VLESVGIHDV LSKSQGSSNP HNVVKATFDA LLQMRSAHTV A KQRGVSLE KVFKG

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #5: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 13.376448 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MNHYETVFIL NPVLSEVQVK ETVTKFEEFL TSRGAEMVSK EDWGLKKMAY EIQNKKSGFY HLFEFKVAGE VLIAFETEFR RDERVMRFL TVSLDKHAIS WAERRRAKLK STKA

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #6: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 18.493707 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MRKRAAKKRP LLPDPRFNDQ LVTRFVNNLM WDGKKSTAFK VFYDAIDIIE TKKQNDEKTS LEIWKDALTN VMPHVEVRSR RVGGATFQI PMQIRPDRKI SMAMKWLILY ARRRNEKSMA QRLASECLAA AKEEGAAVKK RMDTHKMAEA NKAFSHFRF

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #7: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 14.652163 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MYTDPIADYL TRVRNAVAAN HKVVEIPASN LKKEITKILF DQGYILSYKF EQNTVQGSIK IALKYDKDTK EPVIKDIQRI SKPGLRKYA GAAKLPRILN GLGIAIVSTS KGLMTGKQAK QLNVGGEVIC YVY

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #8: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 14.464888 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MGVIHKIGRR KTAVARVYVS EGTGNITVNK KEFATYFPTA TLQYKVLQPL SMTENVNNFD VKVNVYGGGT TGQAEAVRMA LARVMCEVN AENRGILKPE GLLTRDPRMV ERKKFGQKKA RKRFQFSKR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #9: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 11.44664 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MSQKIRIKLK SYDHMLVDKS AEKIVKTVKT TGAVVTGPIP LPTHKKLFTV LRSPHVNKKA REQFEVMSYK RLIDIYSSSS KTIDALMKL ELPSGVEVEI KV

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #10: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 13.700957 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MAKATAKKRK VIVESTGEAH ISSTFNNIII SLTNKKGEVI AWSSAGKMGF RGSKKNTPYA AQMAAEDCSK VALEAGLKKV KVYVKGPGN GRESAIRSIH NGGIEVTEII DVTPMPHNGC RPPKRRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #11: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 14.121425 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MPTIQQLVRT GRTQITKKSK SVALDSCPQR RGVCTRVYTT TPKKPNSAMR KVARVRLTNG NEVNAYIPGE GHNLQEHSIV LVRGGRVKD LPGVRYHIVR GALDTSGVAG RTQRRSKYGA KRPKEAKK

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #12: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 13.734152 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKTVANK KKATK

+
Macromolecule #13: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 10.211011 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MAKESMKARE VKREKTVAKY AEKRKALLEA GDYEGLQRLP KNASPVRLHN RCKLTGRPRG YIRQFGISRV TFREMANNGL IPGVKKASW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #14: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 10.565339 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MYLTKEKKEE IFAQHGDAKN TGKAEGQIAL FTYRISHLTE HLKKNRHDYN TERSLVLLVG KRRALLDYLK RKDINRYREI IKVLNIRK

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #15: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 20.106588 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MSVKIRLQRH GKKGKPFYWV VAADARSKRD GKYLEKIGTY NPNTNPATVE LNLDSIVKWL HQGAQPTDTA RAILSYKGAL LKHHLDGGV RKGALTQEQA DAKLTAWLEA KAGKVDAKKD GLSKAQADAK AKALKAEKEV NDKRIAAAAK AEADAIAAAS A TEEAATEE VAEAAEEAPA AEENNETTEA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #16: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 10.1089 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MEEKRNLRKE RIGVVTSNKM DKSIVISEVR KVKHPLYGKF VLKTKKYVAH DETNDCNIGD TVRISETRPL SKTKCWRLVE ILERAK

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #17: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 11.378475 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MSTIEQSAKG KKDGDIRYLT PLNIETNKTK KYCRFKKSGI KYIDYKDADF LLKFVNEQGK ILPRRLTGTS LKYQRKVSVA VKRARHLAL MPYVADLLK

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #18: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 10.278883 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MARSLKKGPF VHYKLDKKVQ ENVESGKNSV VKTWSRASMI TPDFVGQTIA VHNGRQFVPV YVTENMVGHK LGEFSPTRSF RGHAGAKNK GKK

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #19: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 9.442211 KDa
Recombinant expressionOrganism: Flavobacterium johnsoniae (bacteria)
SequenceString:
MANHKSALKR IRSNEKRRVL NRYQHKTTRN AIKALRLATD KSDAAAKLST VISMIDKLAK KNIIHDNKAS NLKSKLTKHV AKL

UniProtKB: Small ribosomal subunit protein bS20

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 313409
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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