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- EMDB-27011: Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound,... -

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Basic information

Entry
Database: EMDB / ID: EMD-27011
TitleCutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Map data30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Sample
  • Complex: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
    • RNA: x 1 types
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
Keywordsribosome / sarecycline / acne / ANTIBIOTIC
Function / homology
Function and homology information


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / K Homology domain / K homology RNA-binding domain ...Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 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. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / 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 S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
30S ribosomal protein S10 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsLomakin IB / Devarkar SC / Bunick CG
Funding support United States, 1 items
OrganizationGrant numberCountry
Almirall, LLC United States
Citation
Journal: 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.
#1: Journal: To be published
Title: The structure of the Cutibacterium acnes 70S ribosome
Authors: Lomakin IB / Devarkar SC / Grada A / Bunick CG
History
DepositionMay 18, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27011.png

Downloads & links

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Map

FileDownload / File: emd_27011.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
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: 0.15
Minimum - Maximum-0.51722646 - 1.2212384
Average (Standard dev.)0.00025542837 (±0.030647634)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: 30S ribosomal subunit with Sarecycline bound, head domain...

Fileemd_27011_half_map_1.map
Annotation30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 30S ribosomal subunit with Sarecycline bound, head domain...

Fileemd_27011_half_map_2.map
Annotation30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA ...

EntireName: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Components
  • Complex: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
    • RNA: 16S ribosomal RNA
    • Protein or peptide: 30S ribosomal protein S5
    • 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
  • Ligand: Sarecycline
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA ...

SupramoleculeName: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Cutibacterium acnes (bacteria)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / 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

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Macromolecule #2: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 7 / 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

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Macromolecule #8: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 8 / 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

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Macromolecule #9: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 9 / 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

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Macromolecule #10: Sarecycline

MacromoleculeName: Sarecycline / type: ligand / ID: 10 / Number of copies: 1 / Formula: V7A
Molecular weightTheoretical: 487.502 Da
Chemical component information

ChemComp-V7A:
Sarecycline / medication, antibiotic*YM

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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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

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Image processing

Particle selectionNumber selected: 1108852
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Local 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)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8cvo:
Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

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