[English] 日本語
Yorodumi
- EMDB-26959: Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26959
TitleCutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Map data70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Sample
  • Complex: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
    • RNA: x 5 types
    • Protein or peptide: x 49 types
  • Ligand: x 4 types
Keywordsribosome / sarecycline / acne / ANTIBIOTIC
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation ...small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein S6 superfamily / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 30S ribosomal protein S10 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 ...50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 30S ribosomal protein S10 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS13 / 50S ribosomal protein L35 / Large ribosomal subunit protein uL5 / AURKAIP1/COX24 domain-containing protein
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLomakin IB / Devarkar SC / Bunick CG
Funding support United States, 1 items
OrganizationGrant numberCountry
Almirall, LLCresearch grant United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.
Authors: Ivan B Lomakin / Swapnil C Devarkar / Shivali Patel / Ayman Grada / Christopher G Bunick /
Abstract: Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, ...Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
History
DepositionMay 12, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26959.png

Downloads & links

-
Map

FileDownload / File: emd_26959.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 340 pix.
= 363.12 Å		1.07 Å/pix.
x 340 pix.
= 363.12 Å		1.07 Å/pix.
x 340 pix.
= 363.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5512391 - 1.51766
Average (Standard dev.)0.0055122683 (±0.06892903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 363.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

Fileemd_26959_half_map_1.map
Annotation70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

Fileemd_26959_half_map_2.map
Annotation70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

EntireName: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Components
  • Complex: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
    • RNA: RNA (1537-MER)
    • 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 S8
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein bS22
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type Z
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • 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 L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • 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 L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L31
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein bL37
    • RNA: 32MF mRNA
    • RNA: P-site initiator tRNA
    • Protein or peptide: 50S ribosomal protein L36
  • Ligand: Sarecycline
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

+
Supramolecule #1: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

SupramoleculeName: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54
Source (natural)Organism: Cutibacterium acnes (bacteria)

+
Macromolecule #1: RNA (1537-MER)

MacromoleculeName: RNA (1537-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 498.742875 KDa
SequenceString: UUUUUCAUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUGCUUUUG UGGGGUGCUC GAGUGGCGAA CGGGUGAGUA ACACGUGAGU AACCUGCCCU UGACUUUGGG AUAACUUCAG G AAACUGGG ...String:
UUUUUCAUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUGCUUUUG UGGGGUGCUC GAGUGGCGAA CGGGUGAGUA ACACGUGAGU AACCUGCCCU UGACUUUGGG AUAACUUCAG G AAACUGGG GCUAAUACCG GAUAGGAGCU CCUGCUGCAU GGUGGGGGUU GGAAAGUUUC GGCGGUUGGG GAUGGACUCG CG GCUUAUC AGCUUGUUGG UGGGGUAGUG GCUUACCAAG GCUUUGACGG GUAGCCGGCC UGAGAGGGUG ACCGGCCACA UUG GGACUG AGAUACGGCC CAGACUCCUA CGGGAGGCAG CAGUGGGGAA UAUUGCACAA UGGGCGGAAG CCUGAUGCAG CAAC GCCGC GUGCGGGAUG ACGGCCUUCG GGUUGUAAAC CGCUUUCGCC UGUGACGAAG CGUGAGUGAC GGUAAUGGGU AAAGA AGCA CCGGCUAACU ACG(PSU)GCCAGC AGCC(G7M)CGGUG AUACGUAGGG UGCGAGCGUU GUCCGGAUUU AUUGGGCG U AAAGGGCUCG UAGGUGGUUG AUCGCGUCGG AAGUGUAAUC UUGGGGCUUA ACCCUGAGCG UGCUUUCGAU ACGGGUUGA CUUGAGGAAG GUAGGGGAGA AUGGAAUUCC UGGUGGAGCG GUGGAAUGCG CAGAUAUCAG GAGGAACACC AGUGGCGAAG GCGGUUCUC UGGGCCUUUC CUGACGCUGA GGAGCGAAAG CGUGGGGAGC GAACAGGCUU AGAUACCCUG GUAGUCCACG C UGUAAACG GUGGGUACUA GGUGUGGGGU CCAUUCCACG GGUUCCGUGC CGUAGCUAAC GCUUUAAGUA CCCCGCCUGG GG AGUACGG CCGCAAGGCU AAAACUCAAA GGAAUUGACG GGGCCCCGCA CAAGCGGCGG AGCAUGCGGA UUAAUUCGAU (2MG)(5MC)AACGCGU AGAACCUUAC CUGGGUUUGA CAUGGAUCGG GAGUGCUCAG AGAUGGGUGU GCCUCUUUUG GGG UCGGUU CACAGGUGGU GCAUGGCUGU CGUCAGCUCG UGUCGUGAGA UGUUGGGUUA AGUCCCGCAA CGAGCGCAAC CCUU GUUCA CUGUUGCCAG CACGUUAUGG UGGGGACUCA GUGGAGACCG CCGGGGUCAA CUCGGAGGAA GGUGGGGAUG ACGUC AAGU CAUCAUGCCC CUUAUGUCCA GGGCUUCACG CAUGCUACAA UGGCUGGUAC AGAGAGUGGC GAGCCUGUGA GGGUGA GCG AAUCUCGGAA AGCCGGUCUC AGUUCGGAUU GGGGUCUGCA ACUCGACCUC AUGAAGUCGG AGUCGCUAGU AAUCGCA GA UCAGCAACGC UGCGGUGAAU ACGUUCCCGG GGCUUGUACA CAC(5MC)G(4OC)C(5MC)GU (5MC)AAGUCAUGA AA GUUGGUA ACACCCGAAG CCGGUGGCCU AACCGUUGUG GGGGAGCCGU CGAAGGUGGG ACUGGUGAUU AGGACUAAGU CG (UR3)AACAAG GUAGCCGUAC C(2MG)G(MA6)(MA6)GGUGC GGCUGGAUCA CCUCCUUUCU AAGGAG

GENBANK: GENBANK: CP059593.1

+
Macromolecule #49: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 49 / Number of copies: 1
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 1.002554625 MDa
SequenceString: GCAAAGUUGU GUAGUGCGAU CGGUGGAUGC CUUGGCACCA AGAGCCGAUG AAGGACGUUG UGACCUGCGA UAAGCCCUGG GGAGUUGGU GAGCGAGCUG UGAUCCGGGG GUGUCCGAAU GGGGAAACCU GGAAUGUCCG GAGUAGUGUC CGGUGGCCCU G CCCUGAAU ...String:
GCAAAGUUGU GUAGUGCGAU CGGUGGAUGC CUUGGCACCA AGAGCCGAUG AAGGACGUUG UGACCUGCGA UAAGCCCUGG GGAGUUGGU GAGCGAGCUG UGAUCCGGGG GUGUCCGAAU GGGGAAACCU GGAAUGUCCG GAGUAGUGUC CGGUGGCCCU G CCCUGAAU GUAUAGGGGU GUGGGUGGUA ACGCGGGGAA GUGAAACAUC UUAGUACCCG UAGGAAGAGA AAACAAGUGU GA UUCCGUG AGUAGUGGCG AGCGAAAGCG GAGGAGGCUA AACCGUGUGU GUGUUCAAGC CGGCAGGUGU UGCAUGUGCG GGG UUGUGG GGGCCUUGUG GUUCUGCUGC CGCAGGAUUG GCCAGUGAGA AAUGUUGCGU GAAGGUGAAG CGUCUGGGAA GGCG UACCG GAGUGGGUGA GAGUCCUGUA ACUGUAAGCG UGGCACUGGU GUGGGGUUGC CCCGAGUAGC GUGGGACUCG UGGAA UUUC GCGUGAAUCU GGCGGGACCA CCCGUCAAGC CUAAAUACUC CUUGGUGACC GAUAGUGGAU GAGUACCGUG AGGGAA GGG UGAAAAGUAC CCCGGGAGGG GAGUGAAAGA GUUCCUGAAA CCGGUCGCAU GCAAGCCGUC AGAGCCUGUG UGGUGAU GG CGUGCCUUUU GAAGAAUGAG CCUGCGAGUU AGUGAUGCGU GGCGAGGUUA ACCCGUGGUG GGGGAGUCGU AGCGAAAG C GAGUCCGAUA AGGGCGUGAG UCGCGUGUUC UAGACCCGAA GCGGUGUGAU CUAUCCAUGG CCAGGAUGAA GCGUCGGUA AGACGUCGUG GAGGUCCGAA CCCACUUCAG UUGAAAAUGG AGGGGAUGAG UUGUGGAUAG GGGUGAAAGG CCAAUCAAAC ACCGUGAUA GCUGGUUCUC CCCGAAAUGC AUUUAGGUGC AGCGUUGCGU GGUUCUUGUU GGAGGUAGAG CACUGGAUGG U CUAGGGGG CUUAUCGGCU UACCGAAAUC AGCCAAACUC CGAAUGCUGG CAAGUGUAGC GUGGCAGUGA GACGGCGGG (PSU)GAUAAGCUU CGUCGUCGAG AGGGAAACAG CCCAGAUCAU CAGCUAAGGC CCCUAAGUGG UGACUCAGUG GGAAAG GAU GUGGAGUUGC GUAGACAACC AGGAGGUUGG CUUGGAAGCA GCCAUCCUUG AAAGAGUGCG UAAUAGCUCA CUGGUCA AG UGAUUCCGCG CCGAUAAUGU AGCGGGGCUU AAGUUAUCCG CCGAAGCUGU GGCAACCUGU GUGGUUGGGU AGGGGAGC G UCGUGUCAGU GGUGAAGCUG CCGGGUGACU GUGUGGUGGA GUUGAUGCGA GUGAGAAUGC AGGCAUGAGU AGCGUGUGA CGGGUGGGAA UCCCGUCCGC CGAUUAUCCA AGGGUUCCAG GGUCAAGUUU GUCUGCCCUG GGUGAGUCGG GUCCUAAGGC GAGGCCGAC AGGCGUAGUC GAUGGGUAAC CAGUUGAUAU UCUGGUACCG GCUUGUCACC GUCCGUGUCG AGGUGUGUGA U GCUAAGCA UGUGAGCUUG UCUUGGGAGU GUUUUUGAUG CUUCUGGGGU GGGUGAGUGU GUGAACCGAU CAUGUAGUAG GC AAGCUGC GGAGGGACGC AGUGAGGUAG CUCAUCCCCG GUGAUGGUUG UCCGGGGCUA AGUGUGUGGA CUGUCUGGUA GGU AAAUCC GCUGGGCGUG AAGGUUGAGG CAUGAUGGGG AGCCCAUGGU UGUGGGUGAG UGAGUGAUCC UGUACUGUCG AGAA AAGCU UCGUGAGCGA GGUGGCGGGU CCGCCCGUAC CCUAAACCGA CACUGGUGGA UAGGUAGAGU AUACCGAGGC GAUCG AGUG AAUCGUGGUG AAGGAACUCG GCAAAAUGCC CCCGUAACUU UGGGAUAAGG GGGACCUGAG CUGUCGUGCA CCCGUG CGG UGUGGUGGCG GUGAGGGGCG CAGAGUCCAG GGGGAAACGA CUGUUUACCA AAAACACAGG UCCGUGCGAA GUCGUAA GA CGAUGUAUAC GGACUGACUC CU(2MG)CCCGGUG CUGGAAGGUU AAGGGGAACU GUGAGUGUAU GCGUAGCGGU GAAC UUAAG CCCCAGUAAA CGGCGGUGG(PSU) AAC(3TD)A(PSU)AACC AUCCUAAGGU AGCGAAA(5MU)UC CUUGUCGGG UAAGUUCCGA C(5MC)UGCACGAA UGGAGUAACG AUUUCCCUAC UGUCUCCACC AUGAACUCGG UGAAAUUGCA UUACGA GUA AAGAUGCUCG UUACGCGCAG CAGGACGGAA AGACCCCGGG ACCUUUACUA UAGUUUGGUA UUGGUGAUUG GGACGGU UU GUGUAGGAUA GGUGGGAGAC GUUGAUGCGG CCACGCUAGU GGUGGUGGAG UCGUUGGUGA AAUACCACUC UGAUUGUU C UGGUUAUCUC ACUGUGGACC GUGAUCCGGU UCAAGGACAG UGCCUGAUGG GUAGUUUGAC UG(OMG)GGCGGUC GCCUC CUAA AGGGUAACGG AGGCGCCCAA AGGUUCCCUC AGCCUGGUUG GUAAUCAGGU GGUGAGUGUA AGUGCACAAG GGGGCU UGA CUGUGAGACU GACAGGUCGA GCAGGGACGA AAGUCGGGAC UAGUGAUCUG ACGGUGGCUU GUGGAUGCGC CGUCACU CA ACGGAUAAAA GGUACCCCG(2MG) GGA(H2U)AACAGG C(PSU)GAUCUUGC CCGAGCGCUC AUAGCGACGG CAUGGU UUG GCA(OMC)CUCG(2MA)(PSU) GUCGGCUCGU CGCAUCCUGG GGCUGGAGUC GGUCCCAAGG GUUGGGC(OMU)GU U CGCCCAUU AAAGCGGCAC GCGAGC(PSU)GGG UUCAGAACGU CGUGAGACAG (PSU)(PSU)CGGUCCCU AUCCGCUGCG CGCGGAGGA AUCUUGAGAA GGGCUGUCUU UAGUACGAGA GGACCGAGAC GGACUGACCU CUGGUGUGCC AGUUGUUCUG C CAAGAGCA UGGCUGGUUG GCUACGUCGG GUUGUGAUAA CCGCUGAAAG CAUCUAAGCG GGAAGCACGC UUCAAGAUAA GG GUUCCCA CAGGAGUGUU CCUGGUAAGG UCCCCGAGAG AUGAUCGGGU UGAUAGGCCA GACGUGGACG CAUCGUAAGG UGU GGAGCU GACUGGUACU AAUAGACCGA GGACUUUCAU UAACA

+
Macromolecule #50: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 50 / Number of copies: 1
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 38.770055 KDa
SequenceString:
UUUCCGGUGG CCAUAGUGGA AGGGAAACAC CCGGUCCCAU UCCGAACCCG GUCGUUAAGC CUUCCAACGC UGAUGGUACU GCACGAGGG AUCGUGUGGG AGAGUAAGAC GCUGCCGGAA U

GENBANK: GENBANK: CP059593.1

+
Macromolecule #52: 32MF mRNA

MacromoleculeName: 32MF mRNA / type: rna / ID: 52 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.115308 KDa
SequenceString:
CAAGGAGGUA AAAAUGUUUU AA

+
Macromolecule #53: P-site initiator tRNA

MacromoleculeName: P-site initiator tRNA / type: rna / ID: 53 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.846902 KDa
SequenceString:
CGCGGGG(4SU)GG AGCAGCCUGG UAGCUCGUCG GG(5MC)UCAUAAC CCGAAGGUCG UCGG(5MU)(PSU)CAAA UCCG GCCCC CGCAACCA

GENBANK: GENBANK: CP009106.1

+
Macromolecule #2: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 23.271605 KDa
SequenceString: MARYTGPLTK KSRRLGTDLV GNDKSFERRP YPPGVHGRGR TKDSEYSLQL REKQKARYAY GVLEKQFRRY YEEADRAQGK TGDVLLQIL ESRLDNVVYR AGLAATRRQA RQMVSHGHFL VNGKKVNIPS YRVSTHDIID VREKSKDLPP IVIARETFET R DVPAWLEV ...String:
MARYTGPLTK KSRRLGTDLV GNDKSFERRP YPPGVHGRGR TKDSEYSLQL REKQKARYAY GVLEKQFRRY YEEADRAQGK TGDVLLQIL ESRLDNVVYR AGLAATRRQA RQMVSHGHFL VNGKKVNIPS YRVSTHDIID VREKSKDLPP IVIARETFET R DVPAWLEV RPNKGRILVH QLPTRDQIVI DVNEQAIVEL YSK

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #3: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 22.603695 KDa
SequenceString: MSGTQRRGGG AGGERRGRDN RRGQNDRNRN QNEYLERVVA INRVAKVVQG GRRFSFTALV VVGDGEGSVG VGYGKAKEVP AAIAKAVEE AKKHFFKVPL VGRTITHPVI GEKAAGVVML RPASPGTGVI AGGSARAVLE CAGVHDVLAK SLGSSNAINV V HATVDALQ ...String:
MSGTQRRGGG AGGERRGRDN RRGQNDRNRN QNEYLERVVA INRVAKVVQG GRRFSFTALV VVGDGEGSVG VGYGKAKEVP AAIAKAVEE AKKHFFKVPL VGRTITHPVI GEKAAGVVML RPASPGTGVI AGGSARAVLE CAGVHDVLAK SLGSSNAINV V HATVDALQ QLEEPEEVAR RRGKSVEDIA PAAMLRARKE ADEAAAAARM EEKAGVN

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #4: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.270147 KDa
SequenceString:
MRKYEVMIII DPTVEERQVD SLMEKYLKVI TDEKGTVDNV DVWGKRRLAY DIQKKSEGIY VVVNATCEPA TIQELDRLLA IDEKIMRTK VMRPEIH

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #5: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 14.67793 KDa
SequenceString:
MTMTDPIADM LTRLRNANQA YHDQTSMPHS KIKAGIAGIL KSEGYIADYK VNEPKEGEVG KTLTLTLKYG ENRERSIAGV RRISKPGLR VYAKSTALPK VLGGLGIAII STSQGLLTDK QAHEKSVGGE VLAYVW

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #6: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 14.194463 KDa
SequenceString:
MATAGHKGAP KTKVRRKEKK NVVAGQAHIK STFNNTIIAI TDPSGAVISW ASAGTVGFKG SRKSTPFAAQ MAAEAAGRRA MEHGMKRVD VFVKGPGSGR ETAIRSLGAV GLEIGPISDV TPVPHNGCRP PKRRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #7: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.666084 KDa
SequenceString:
MPTIQQLVRK GRTDKISKNK TPALKGSPQR RGVCTRVYTT TPKKPNSALR KVARVRLSSG IEVTAYIPGV GHNLQEHSMV LVRGGRVKD LPGVRYKIVR GSLDTQGVKG RKQARSRYGA KKEK

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #8: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 10.10276 KDa
SequenceString:
MDAAEKKKII EEYATHPGDT GSPDVQVAIL TKRIAELTEH LKVHKGDHHS RRGLMLMVGQ RRRLLNYIAK NDIEHYRELI ARLGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #9: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 10.475277 KDa
SequenceString:
MSENTAERTT RRKVREGLVV SDKMNKTITV MVEDRVKHPL YGKVMTKSVR LKAHDENNEA GMGDRVRIME TRPLSATKRW RLVEIIEKA K

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #10: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 8.817497 KDa
SequenceString:
MAGPQRKSVN KKKVVPIKTV HIGAVDYKDT ALLRKFISER GKIRARRVTG LSVQDQRKVA IAIKNARELA LLPYASTAR

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #11: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 9.724277 KDa
SequenceString:
MPNIKSQIKR VKTNEKSRQR NKAVKSALRT YVRNFRRAAE AGDVEAATKA ARVANRQLDK AASKGVIHKN QAANRKSAIS KKLNSLAA

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #12: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 15.980861 KDa
SequenceString:
MATKIRLKRL GKIRTPHYRV VVMDSRAKRD GRAIEEIGQY HPKADPSVIV IDSERVQYWL GVGAQPTEAV VALLKRTGDW QKFTGDTSP SGVKPQPERP NKDDLFNAAL AEADEAPREA ITKKSEGAAA DEASESAAGD NSGEKAEA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #13: 30S ribosomal protein bS22

MacromoleculeName: 30S ribosomal protein bS22 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 4.120248 KDa
SequenceString:
MGSVIKKRRK RMAKKKHRKL LKRTRIQRRR AGK

UniProtKB: AURKAIP1/COX24 domain-containing protein

+
Macromolecule #14: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 29.728719 KDa
SequenceString: MGQKINPHGF RLGVTTDHKT RWYAEKQYAE LVGEDVKIRE WLHKNLERAG LSSIEIERRS ERVTIFLYAA RPGIVIGRNG AEAERVRGE LEKLTGKQIQ LNILEVKSPE TDAQLVAQGI AEQLAARVAF RRAMRKAQQS AMNAGALGIR IKCSGRLGGA E MSRSEGYR ...String:
MGQKINPHGF RLGVTTDHKT RWYAEKQYAE LVGEDVKIRE WLHKNLERAG LSSIEIERRS ERVTIFLYAA RPGIVIGRNG AEAERVRGE LEKLTGKQIQ LNILEVKSPE TDAQLVAQGI AEQLAARVAF RRAMRKAQQS AMNAGALGIR IKCSGRLGGA E MSRSEGYR EGRVPLHTLR ADIDYGFFEA RTTFGRIGVK VWIYKGDVTG TRAERAAQKA ARQAAQGGRG GRGGNRRGRG DR PDRRGGR RRAEAAKQSA ETPAPQTENA GA

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #15: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 17.615482 KDa
SequenceString:
MPRKGPAPKR PVMVDPVYGS PLVSQLVSKI LLDGKKTVAQ NIVYTALEGC RAKNNTDPVQ TLKRALDNIK PSLEVKSRRV GGATYQVPV EVKPARQTTL AMRWLVNFSR ERREKTMAER LMNEILDASN GLGASVKRRE DTHKMAEANR AFAHYRW

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #16: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 18.630139 KDa
SequenceString:
MTDTPTENLE NTEVTPFTEG DREIAYRTDS NPTVAAGDSK RPAMIAPGAA TGRRKEAIAR VRITPGSGQW KINGRTLEDY FPNKVHQQI VTEPFATAGV EGAYDVIARI GGGGVTGQAG ALRLGIARAL NNVDPEASRP ALKKAGMLTR DARVKERKKA G LKKARKAP QYSKR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #17: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.750766 KDa
SequenceString:
MAGQKIRIRL RAYDHEVIDS SARKIVDTVT RTGAKVAGPV PLPTEKNVFC VIRSPHKYKD SREHFEMRTH KRLIDILEPT PKTVDSLMR LDLPAGVDIE IKLP

UniProtKB: 30S ribosomal protein S10

+
Macromolecule #18: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 14.030231 KDa
SequenceString:
MARLIGVDLP RDKRLEVALT YIYGIGRTRA TETLKATGIS GDLRVHELTD DQLVALRDHI EANYHVEGDL RREVAADIRR KIEIGTYQG RRHRSGLPVR GQRTRTNART RKGKRKAVAK KKAK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #19: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.924359 KDa
SequenceString:
MAKTALKVKA ARKPKFGVRA YTRCQRCGRP HSVYRKFGLC RICLREMAHA GQLPGVTKSS W

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #20: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 10.536264 KDa
SequenceString:
MPRSLKKGPF VDEHLAKKVT AQNEAGTHNV IKTWSRRSMV TPDMIGHTIG VHDGRKHVPV FVTESMVGHK LGEFAPTRTF KGHVKDDKK ARRR

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #21: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 31.583166 KDa
SequenceString: MAVVTTRQLL ESGVHFGHQT RRWNPKMKRF IFTERNGIYI IDLHQSLTYI DKAYAFVKET VAKGGQILFV GTKKQAQESI VEQATRVGM PYVNQRWLGG MLTNFQTISK RIARLKELEA MDFDKVSGSG LTKKELLMLS REKDKLEKDL GGIRDMPKVP Q AVWVVDTK ...String:
MAVVTTRQLL ESGVHFGHQT RRWNPKMKRF IFTERNGIYI IDLHQSLTYI DKAYAFVKET VAKGGQILFV GTKKQAQESI VEQATRVGM PYVNQRWLGG MLTNFQTISK RIARLKELEA MDFDKVSGSG LTKKELLMLS REKDKLEKDL GGIRDMPKVP Q AVWVVDTK KEHLAIDEAR KLKIPVVAIL DTNCDPDEVD YAIPGNDDAI RSVSLLTRII ADAAAEGLMA RSAGKSGEQP AE AEPMPDW ERELLEGDGA KTEAKAEEPK AEAKKADEAP EAEKSN

UniProtKB: Small ribosomal subunit protein uS2

+
Macromolecule #22: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 30.309863 KDa
SequenceString: MGIRKYKPTT PGRRGSSVSD FVELTRSTPE KSLLVAKPKT GGRNNTGRIT TRHIGGGHKQ AYRIIDFKRY DKDGVPAKVA HIEYDPNRT ARIALLHYAD GEKRYIIAPD GVGQGTVVVS GPEADIKPGN NLPLRNIPVG TTVHAVELRP GGGAKMGRSA G ASVQLVAR ...String:
MGIRKYKPTT PGRRGSSVSD FVELTRSTPE KSLLVAKPKT GGRNNTGRIT TRHIGGGHKQ AYRIIDFKRY DKDGVPAKVA HIEYDPNRT ARIALLHYAD GEKRYIIAPD GVGQGTVVVS GPEADIKPGN NLPLRNIPVG TTVHAVELRP GGGAKMGRSA G ASVQLVAR EGKYATVRLP SGEMRMVDIR CRATIGEVGN AEQININWGK AGRNRWKGIR PTVRGVVMNP IDHPHGGGEG RT SGGRHPV SPWGKPEGRT RNKKKASSRL IVRRRKSGKK R

UniProtKB: Large ribosomal subunit protein uL2

+
Macromolecule #23: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 23.553053 KDa
SequenceString: MTNERTVKGV LGTKLGMTQL WDEHNRLVPV TVIQAGPCVV TQVRTPETDG YSAVQLGYGA VKAKNVTKPE AGHFEKAGVT PRRHLVELR TADASEYTLG QEIAADVFSE SDFVDVTGTS KGKGTAGVMK RHGFGGLRAT HGVHRKHRSP GSIGGCSTPG K VIKGLRMA ...String:
MTNERTVKGV LGTKLGMTQL WDEHNRLVPV TVIQAGPCVV TQVRTPETDG YSAVQLGYGA VKAKNVTKPE AGHFEKAGVT PRRHLVELR TADASEYTLG QEIAADVFSE SDFVDVTGTS KGKGTAGVMK RHGFGGLRAT HGVHRKHRSP GSIGGCSTPG K VIKGLRMA GRMGVERVTV QNLQVHSVDA ERGIMLVRGA VPGPKGSLLV VRSAAKKAAK NGDAA

UniProtKB: Large ribosomal subunit protein uL3

+
Macromolecule #24: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 32.34217 KDa
SequenceString: MNETKTIDVL DVKGKKAGSA ELPGDLFDVN TNIPLIHQVV VAQLAAARQG THATKTRGQV SGGGKKPWRQ KGTGRARQGS TRAPQWVGG GTVHGPQPRS YAQRTPKKMV GAALRGALSD MARDNRIFVV TSLVDGDKPS TKQAKAVLSG LAELRKVLVV L DRSDEIDW ...String:
MNETKTIDVL DVKGKKAGSA ELPGDLFDVN TNIPLIHQVV VAQLAAARQG THATKTRGQV SGGGKKPWRQ KGTGRARQGS TRAPQWVGG GTVHGPQPRS YAQRTPKKMV GAALRGALSD MARDNRIFVV TSLVDGDKPS TKQAKAVLSG LAELRKVLVV L DRSDEIDW LSVRNLSEVH VLAADQLNTY DVVNARTIVF SQAGLDAFVG ARSANTQALS AEPEVPETNV ADQHPYGEDS FR GDNPPAG FDIKGNEDSM KFHEPSSPWY GRTIAEVWFR SAAAAEAAGF VNAVKSDSEK EDAK

UniProtKB: Large ribosomal subunit protein uL4

+
Macromolecule #25: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 23.901756 KDa
SequenceString: MSTDAIAHEM PRLKKQYREQ IRAAMQEEFG YRNPMLIPGL EKIVVNMGVG DAAHDSKVMD GAIRDITAIT GQKPQVTKAR KSIAQFKLR EGQPIGCHVT LRGDRMWEFA DRLLTLALPR IRDFRGLNSN QFDGKGNYTF GLSEQVMFLE IDQDKIDRIR G MDITFVTT ...String:
MSTDAIAHEM PRLKKQYREQ IRAAMQEEFG YRNPMLIPGL EKIVVNMGVG DAAHDSKVMD GAIRDITAIT GQKPQVTKAR KSIAQFKLR EGQPIGCHVT LRGDRMWEFA DRLLTLALPR IRDFRGLNSN QFDGKGNYTF GLSEQVMFLE IDQDKIDRIR G MDITFVTT AQTNEEGKAL LKHLGFPFKA KDDPKKAKTK RGPAYYAKKK KK

UniProtKB: Large ribosomal subunit protein uL5

+
Macromolecule #26: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 19.868811 KDa
SequenceString:
MSRIGRLPIA VPSGVEVKLD GQYVEVKGPK GTLNFTVREP ITVSKNDEGA ILVERPDDER ENRSLHGLTR TLINNMVIGV TEGYEKKLE IQGVGYRVLS KGPKQLEFNL GFSHPVIVDA PEGITFAVEN PTKFSVQGID KQVVGETAAN IRKIRKPEPY K GKGVRYEG ENVRRKVGKA GK

UniProtKB: Large ribosomal subunit protein uL6

+
Macromolecule #27: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 16.325824 KDa
SequenceString:
MTTYSPKAGE VQRKWYVIDA EDIVLGRLAT TAANLLRGKH KPQYAPHIDT GDFVVVVNAS KIALTGKKAT DSLRYDHSGR PGGLRVTSI GEMLAKNPRR AVERAVWGMM PKNKLSRQQL KKLKVYGGPE HPHAAQNPQP YEITQIAQ

UniProtKB: Large ribosomal subunit protein uL13

+
Macromolecule #28: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.503871 KDa
SequenceString:
MIQQETRLKV ADNTGAKELL CIRVLGGSKR RYAYLGDTIV CTVKDAIPGG NVKKGEVVKA VVVRTVKSHR RPDGSYIKFD ENAAVLLKG DGEPRGTRIF GPIARELREK KFMRIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #29: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 15.542903 KDa
SequenceString:
MAIELHDLKP APGAHKAKTR VGRGEGSKGK TAGRGTKGTG ARKNVPEFFA GGQMPIHMQA PKLGGFHNPF RTEYQVVNLD KVEALFPKG GKITVDDLVS VGAVRDNELV KVLGTGELTV KVDLVVDAWS KSAQEKIEKA GGSVTKR

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #30: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 15.700248 KDa
SequenceString:
MLIPRRVKYR KQHHPKRTGA AKGGTQLAFG DYGIQATEGG YLTNRQIEAA RIAMTRYIKR GGKVWINVYP DRPMTKHPAE SRMGSGKGT PEWWIANIKP GRVLFELSGV PEDVAREAMR LAIHKLPMKA RFISREGGDN

UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #31: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 20.058641 KDa
SequenceString:
MPKPTKGPRL GGSPAHERII LRNLASQLFE HGRVVTTVTK AKRVRPLAEK LINRAKTDTV ANRRFVNRTI TDRGIVHILF TEIGPRMEG RDGGYTRVTR IGIRKGDNAP MAVIEVISDK VAPKAPASAA DAKAQINTAT EAKDAEPEAG DAAVEHNAPA E DAAAQAPV ADEQEAAEAD EKAEEKPEA

UniProtKB: 50S ribosomal protein L17

+
Macromolecule #32: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.727841 KDa
SequenceString:
MASTLTVRKS LSDRAKARAR RQARGRKKIF GTVERPRMVV TRSSKHVFVQ VIDDVAGNTL VSASTMEAEL REMSGDKTAK AARVGTIIG ERAKAAGITK VVFDKAGNQY HGRIAALADA AREAGLDF

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #33: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.106117 KDa
SequenceString:
MSNIIDEIDK ASMRDDIPEF RPGDSVKVHV KVVEGSRTRV QVFSGIVISR TGGGVQESFT VRKLSFGTGV ERTFPLHSPI IDKIEVDRH GAVRRAKLYY LRGRRGKAAK IKERGSAR

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #34: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.988012 KDa
SequenceString:
MARVKRSVNA KKKRREVLDQ ASGYRGQRSR LYRKAKEQTL HSATYSFRDR RAKKGDFRSL WIQRINAASR AQGMTYNRFI NGLKNAGVE VDRKMLAELA VSDINAFNSL VEVAKASQPQ NAAA

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #35: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.087788 KDa
SequenceString:
MYAIVRSGGR QHKVAVGDVV EIDKVADEAG SSIELTPLLV VDGESVTSDK DALGKVKVTA EVLGETKGPK IRILKYKNKT GYKKRQGHR QKYTQVKVTG IEG

UniProtKB: 50S ribosomal protein L21

+
Macromolecule #36: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 16.729471 KDa
SequenceString:
MSKTERPSRR AALLGDRPGS YAIARHVRMS ASKCRRVINL VRGMDAVDAV TMLKFQPQAA AEPIRKVIAS AMANAEQTEG LRADDLYIS QAFVDEGITM RRIRPRAKGS ASRILKRSAH ITVVVEPKEA RQARKKAKSG RPAAAAKSET EKGA

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #37: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 11.34922 KDa
SequenceString:
MSELKIRDPR DIILAPVVSE KSYGLLDQNT YTFVVKPTAN KTEIKIAIEQ IFGVKVTSVN TMNRKGKVRR TRTGVGKRPD TKRAIVTVA EGDRIDIFTG PVA

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #38: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 13.514626 KDa
SequenceString:
MKSLKIKKGD RVKVIAGNDK GAIGEVLSVD PARERVVVEG VNIRKHHRRD MPTPQGGTTK GGIISSEAPI HVSNVQLVTK IDGKDVVTR VGYRRVDVTK RRPDGSEYAA QRSVRYLKKE EAK

UniProtKB: 50S ribosomal protein L24

+
Macromolecule #39: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 22.349113 KDa
SequenceString: MADIIHLKAE QRTEFGKGAA RRIRRDDKVP AVMYGHDHDP IHVTLDGHAT LLALRTENPL LSIEIEGQKP MLALPKDVQR DVLKGFVRH VDLLTVRRGE KVDVNVALRI TGESAPGTIA MTEFNEIEVQ ADLLNIPEVI EIDVTGLEAG TTIYLGDLKL P EGTSLLGD ...String:
MADIIHLKAE QRTEFGKGAA RRIRRDDKVP AVMYGHDHDP IHVTLDGHAT LLALRTENPL LSIEIEGQKP MLALPKDVQR DVLKGFVRH VDLLTVRRGE KVDVNVALRI TGESAPGTIA MTEFNEIEVQ ADLLNIPEVI EIDVTGLEAG TTIYLGDLKL P EGTSLLGD AEDVAATVAF PETEPVEDEE SAGEDAQGES EEKAAKE

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #40: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 9.540655 KDa
SequenceString:
MAHKKGASSS RNGRDSNAQR LGVKRFGGQL VNAGEIIVRQ RGTHFHPGDG VGRGGDDTLF ALRDGNVEFG TRRGRRVVNV TPVEAPVEA

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #41: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.953212 KDa
SequenceString:
MAAVCDICAK RPGFGHNVPW SKKKTNRRWS PNIQRVRVVE NGTHKRMNVC TSCLKAGRVS R

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #42: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 8.899072 KDa
SequenceString:
MPKLSAAELR QLSGEELRNK VRELKEELFG LRFQSATGQL ENTARLREVR KDIARVYTVL QERNLNIVDD PDSTKEA

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #43: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.932171 KDa
SequenceString:
MSKLKITQIK SGIATKPNHR ETLRSLGLKR IGDTVIKEDR PEFRGMVRTV RHLVTMEEVD

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #44: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.991128 KDa
SequenceString:
MAVPKRKMSR SNTRHRRSQW KTVATKLVTC ANPACGEKHL PHTACPSCGG YGPRGDRRQV VEA

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #45: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 6.725948 KDa
SequenceString:
MAKKSGDVRP KITLACTECK ERNYITKKNR RNNPDRMEMA KFCPRCRKHT AHRETR

UniProtKB: Large ribosomal subunit protein bL33

+
Macromolecule #46: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 5.185076 KDa
SequenceString:
MKRTFQPSNR RRARNHGFRS RMSTRAGRSI LAARRRKGRV NLSA

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #47: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 7.457868 KDa
SequenceString:
MPKMKSHSGT KKRFKVTGSG KVTARKAGKR HLNEHKSSRV TRRLTGETVL SKGEAAKVKK LLAGHPGR

UniProtKB: 50S ribosomal protein L35

+
Macromolecule #48: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 7.731771 KDa
SequenceString:
MKQGIHPDYR ETTVVCTCGN TFTTRSTSQS GTLNADVCSK CHPFYTGKQK ILDAGGRVAR FERRYGKKN

UniProtKB: Large ribosomal subunit protein bL31

+
Macromolecule #51: 50S ribosomal protein bL37

MacromoleculeName: 50S ribosomal protein bL37 / type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 2.744284 KDa
SequenceString:
MGKTGRKRRA RRKKGANHGK RPNA

+
Macromolecule #54: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 54 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Molecular weightTheoretical: 4.386379 KDa
SequenceString:
MKVQPSVKKI CDKCKVIRRH GRVMVICDNP RHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

+
Macromolecule #55: Sarecycline

MacromoleculeName: Sarecycline / type: ligand / ID: 55 / Number of copies: 2 / Formula: V7A
Molecular weightTheoretical: 487.502 Da
Chemical component information

ChemComp-V7A:
Sarecycline / medication, antibiotic*YM

+
Macromolecule #56: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 56 / Number of copies: 386 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #57: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 57 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #58: water

MacromoleculeName: water / type: ligand / ID: 58 / Number of copies: 129 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.1 sec. / Average electron dose: 30.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1108852
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Non-uniform Refinement / Number images used: 70853
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8crx:
Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound

+
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