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- PDB-10fz: 30S ribosomal subunit from E. coli missing the gene encoding for ... -

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Basic information

Entry
Database: PDB / ID: 10fz
Title30S ribosomal subunit from E. coli missing the gene encoding for the 16S rRNA 2'-O-methyltransferase RsmI
Components
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME / methylation / 30S subunit / helix 44 / RsmI
Function / homology
Function and homology information


transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / regulation of DNA-templated transcription elongation ...transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / regulation of DNA-templated transcription elongation / positive regulation of RNA splicing / transcription elongation factor complex / transcription antitermination / DNA endonuclease activity / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / hydrolase activity / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / : / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / 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 S2, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsBarmada, M.I. / Nandi, S. / Conn, G.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088025 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 AI186518 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM135060 United States
CitationJournal: To Be Published
Title: Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI
Authors: Barmada, M.I. / McGinity, E.N. / Nandi, S. / Dey, D. / Zelinskaya, N. / Harris, G.M. / Comstock, L.R. / Dunham, C.M. / Conn, G.L.
History
DepositionJan 18, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
H: Small ribosomal subunit protein uS8
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
T: Small ribosomal subunit protein bS20
B: Small ribosomal subunit protein uS2
U: Small ribosomal subunit protein bS21
C: Small ribosomal subunit protein uS3
G: Small ribosomal subunit protein uS7
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
S: Small ribosomal subunit protein uS19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)789,44198
Polymers787,56921
Non-polymers1,87177
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1789840096

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Small ribosomal subunit protein ... , 20 types, 20 molecules DEFHKLOPQRTBUCGIJMNS

#2: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V8
#3: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W1
#4: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#5: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W7
#6: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R9
#7: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S3
#8: Protein Small ribosomal subunit protein uS15


Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SSQ8
#9: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3
#10: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG63
#11: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T7
#12: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7
#13: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#14: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68679
#15: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V3
#16: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359
#17: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7X3
#18: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R5
#19: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S9
#20: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG59
#21: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U3

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Non-polymers , 2 types, 109 molecules

#22: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 77 / Source method: obtained synthetically / Formula: Mg
#23: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: small ribosomal subunit from a delta rsmI E. coli strain
Type: RIBOSOME
Details: E. coli 30S subunit lacking Cm1402 modification. This map was generated as part of an EM sample containing the complex of the 16S 2'-O-methyltransferase RsmI and the delta rsmI 30S (PDB ...Details: E. coli 30S subunit lacking Cm1402 modification. This map was generated as part of an EM sample containing the complex of the 16S 2'-O-methyltransferase RsmI and the delta rsmI 30S (PDB 9PZG/EMDB 72071). Particles with no enzyme occupancy were isolated to generate the map of the unbound delta rsmI 30S subunit.
Entity ID: #1-#21 / Source: NATURAL
Molecular weightValue: 0.85 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria) / Strain: delta rsmI
Buffer solutionpH: 7.6
Details: 10 mM HEPES, 10 mM MgCl2, 100 mM NH4Cl, 6 mM Beta-mercaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Recombinant RsmI (1.2 uM), delta-rsmI 30S (0.4 uM), and the SAM analog NM6 (24 uM) were incubated for 30 minutes at 37C to prepare the complex.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 49.27 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8164

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3781314
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58273 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7oe1

7oe1


Accession code: 7oe1 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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