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- EMDB-61625: 50S precursor - Erm complex (C-II) -

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Basic information

Entry
Database: EMDB / ID: EMD-61625
Title50S precursor - Erm complex (C-II)
Map data50S precursor - Erm complex 1
Sample
  • Complex: 50S precursor-Erm complex (C-1)
    • Protein or peptide: x 17 types
    • RNA: x 1 types
Keywords50S precursor / Erm / methyltransferase / antibiotic resistance / ribosome-protein complex / RIBOSOME
Function / homology
Function and homology information


23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome ...23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / ribosome assembly / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal protein L23 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / rRNA adenine N-6-methyltransferase / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Bacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSengupta S / Mukherjee R / Pilsl M / Bagale S / Adhikary AD / Borkar A / Pradeepkumar PI / Engel C / Chowdhury A / Kaushal PS / Anand R
Funding support United Kingdom, India, 3 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Science and Engineering Research Board (SERB) India
Department of Biotechnology (DBT, India) India
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic insights into 50 precursor recognition and targeting by erythromycin resistance methyltransferase.
Authors: Sombuddha Sengupta / Rajat Mukherjee / Michael Pilsl / Siddharam Bagale / Arijit Das Adhikary / Aditi N Borkar / Pushpangadan Indira Pradeepkumar / Christoph Engel / Arindam Chowdhury / Prem ...Authors: Sombuddha Sengupta / Rajat Mukherjee / Michael Pilsl / Siddharam Bagale / Arijit Das Adhikary / Aditi N Borkar / Pushpangadan Indira Pradeepkumar / Christoph Engel / Arindam Chowdhury / Prem S Kaushal / Ruchi Anand /
Abstract: Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive ...Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive precursor ribosomal state. Here, we capture the 50 ribosomal precursor-Erm complex by cryo-EM and show that a transient pocket formed in the early steps of ribosome biogenesis, situated 35 angstrom from the methylation site, serves as an anchor for the auxiliary C-terminal domain of Erm, thereby playing a crucial role in achieving specificity in this short-lived substrate with evolving structural features. Cryo-EM reveals that the catalytic Rossman fold of Erm undergoes a swaying motion to facilitate substrate scouting. Corroboratory smFRET studies show that for effective catalysis, Erm transitions between multiple conformations, an effective strategy adopted to orient the dynamic helix where methylation occurs. Unraveling this unique mechanism of targeting adopted by Erm paves the way for selective design of allosteric inhibitors directed toward reversing MLS resistance.
History
DepositionSep 23, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61625.png

Downloads & links

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Map

FileDownload / File: emd_61625.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S precursor - Erm complex 1
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0136
Minimum - Maximum-0.05338128 - 0.09983214
Average (Standard dev.)0.0003261203 (±0.0041383305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61625_half_map_1.map
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Half map: #1

Fileemd_61625_half_map_2.map
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Sample components

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Entire : 50S precursor-Erm complex (C-1)

EntireName: 50S precursor-Erm complex (C-1)
Components
  • Complex: 50S precursor-Erm complex (C-1)
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L34
    • RNA: 23S ribosomal RNA
    • Protein or peptide: rRNA adenine N-6-methyltransferase
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30

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Supramolecule #1: 50S precursor-Erm complex (C-1)

SupramoleculeName: 50S precursor-Erm complex (C-1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 6.463445 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #2: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 5.397463 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #4: rRNA adenine N-6-methyltransferase

MacromoleculeName: rRNA adenine N-6-methyltransferase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: 23S rRNA (adenine2085-N6)-dimethyltransferase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 28.955529 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MNEKNIKHSQ NFITSKHNID KIMTNIRLNE HDNIFEIGSG KGHFTLELVQ RCNFVTAIEI DHKLCKTTEN KLVDHDNFQV LNKDILQFK FPKNQSYKIF GNIPYNISTD IIRKIVFDSI ADEIYLIVEY GFAKRLLNTK RSLALFLMAE VDISILSMVP R EYFHPKPK ...String:
MNEKNIKHSQ NFITSKHNID KIMTNIRLNE HDNIFEIGSG KGHFTLELVQ RCNFVTAIEI DHKLCKTTEN KLVDHDNFQV LNKDILQFK FPKNQSYKIF GNIPYNISTD IIRKIVFDSI ADEIYLIVEY GFAKRLLNTK RSLALFLMAE VDISILSMVP R EYFHPKPK VNSSLIRLNR KKSRISHKDK QKYNYFVMKW VNKEYKKIFT KNQFNNSLKH AGIDDLNNIS FEQFLSLFNS YK LFNK

UniProtKB: rRNA adenine N-6-methyltransferase

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Macromolecule #5: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 22.277535 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #6: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 22.121566 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #7: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 16.050606 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #8: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.565067 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #9: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.008471 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #10: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 14.393657 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #11: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.159278 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #12: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.528024 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #13: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.586374 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #14: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 12.253359 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #15: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.22216 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #16: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.33925 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #17: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 7.286464 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #18: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 6.55482 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #3: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 941.612375 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAUGUUGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUGCUA A CGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGAA ACGAUGUGGG AA GGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGGC CUG CGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUC UGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA AGCGG GUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAG GCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGGCUAU GU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAGGCGU G AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGAAAUCA GUCGAAGAUA C CAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGCCC GG UGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUAU AAC GGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACC CGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUGAACCUU UACUA UAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UGGAGC CGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGUGGGU AG UUUGACUGGG GCGGUCUCCU CCUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGGAGGU U AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGU GUUUGGCACC UCGAUGUCGG CUCAUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUAUG GCUGUUCGCC A UUUAAAGU GGUACGCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AG GGGGGCU GCUCCUAGUA CGAGAGGACC GGAGUGGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU GGCACUGCCC GGU AGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAA GGGUC CUGAAGGAAC GUUGAAGACG ACGACGUUGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGAGCUAACC GGUAC UAAU GAACCGUGAG GCUUAACCUU

GENBANK: GENBANK: CP063991.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 41.25 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: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 55608
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9jns:
50S precursor - Erm complex (C-II)

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