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- PDB-9zcd: Flavobacterium johnsoniae 30S ribosomal subunit. -

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Basic information

Entry
Database: PDB / ID: 9zcd
TitleFlavobacterium johnsoniae 30S ribosomal subunit.
Components
  • (30S ribosomal protein ...) x 19
  • (Small ribosomal subunit protein ...) x 2
  • 16S rRNA
KeywordsRIBOSOME / 30S
Function / homology
Function and homology information


ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome ...ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 ...: / Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein 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 S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S5, C-terminal domain / 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 / K homology domain-like, alpha/beta / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S13-like, H2TH / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9 / 30S ribosomal protein S1 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS13
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsOrtega, J. / Arpin, D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of a specialized 70S initiation complex.
Authors: Dominic Arpin / Bappaditya Roy / Fawwaz M Naeem / Kurt Fredrick / Joaquin Ortega /
Abstract: Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes ...Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.
History
DepositionNov 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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: 30S ribosomal protein S1
H: 30S ribosomal protein S2
h: 30S ribosomal protein S3
i: 30S ribosomal protein S4
j: 30S ribosomal protein S5
k: 30S ribosomal protein S6
l: 30S ribosomal protein S7
m: 30S ribosomal protein S8
n: 30S ribosomal protein S9
o: 30S ribosomal protein S10
p: 30S ribosomal protein S11
q: Small ribosomal subunit protein uS12
r: 30S ribosomal protein S13
s: 30S ribosomal protein S14
t: 30S ribosomal protein S15
u: Small ribosomal subunit protein bS16
v: 30S ribosomal protein S17
w: 30S ribosomal protein S18
x: 30S ribosomal protein S19
y: 30S ribosomal protein S20
z: 30S ribosomal protein S21
2: 16S rRNA


Theoretical massNumber of molelcules
Total (without water)858,60322
Polymers858,60322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 19 types, 19 molecules AHhijklmnoprstvwxyz

#1: Protein 30S ribosomal protein S1


Mass: 66159.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: SAMN05444388_11595 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6TFV7
#2: Protein 30S ribosomal protein S2


Mass: 28107.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsB, Fjoh_1610 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJG9
#3: Protein 30S ribosomal protein S3


Mass: 27886.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsC, BKM63_03290, DFS20_4233, SAMN05444388_103380 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBX1
#4: Protein 30S ribosomal protein S4


Mass: 22950.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsD, SAMN05444388_103362 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0J7
#5: Protein 30S ribosomal protein S5


Mass: 18206.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsE, SAMN05444388_103369 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0I9
#6: Protein 30S ribosomal protein S6


Mass: 13376.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsF, BKM63_14855, DFS20_3370, SAMN05444388_10494 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7BSW7
#7: Protein 30S ribosomal protein S7


Mass: 18493.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsG, SAMN05444388_103389 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L9G3
#8: Protein 30S ribosomal protein S8


Mass: 14652.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsH, SAMN05444388_103372 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L889
#9: Protein 30S ribosomal protein S9


Mass: 14464.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsI, SAMN05444388_101317 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6R974
#10: Protein 30S ribosomal protein S10


Mass: 11446.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsJ, BKM63_03325, DFS20_4240, SAMN05444388_103387 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CP29
#11: Protein 30S ribosomal protein S11


Mass: 13700.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsK, BKM63_03205, DFS20_4215, SAMN05444388_103363 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBV3
#13: Protein 30S ribosomal protein S13


Mass: 13734.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsM, Z4668, ECs4163 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: P0A7T1
#14: Protein 30S ribosomal protein S14


Mass: 10211.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsN, BKM63_03255, DFS20_4226, SAMN05444388_103373 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0Q7
#15: Protein 30S ribosomal protein S15


Mass: 10565.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsO, SAMN05444388_101497 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QTP8
#17: Protein 30S ribosomal protein S17


Mass: 10108.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsQ, DFS20_4230, SAMN05444388_103377 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8M4
#18: Protein 30S ribosomal protein S18


Mass: 11378.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsR, BKM63_14860, DFS20_3369, SAMN05444388_10495 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U6N1
#19: Protein 30S ribosomal protein S19


Mass: 10278.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsS, DFS20_4235, SAMN05444388_103382 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8S8
#20: Protein 30S ribosomal protein S20


Mass: 9442.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsT, SAMN05444388_102514 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1X2
#21: Protein 30S ribosomal protein S21


Mass: 7433.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsU, BKM63_10790, DFS20_2852 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CKJ9

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Small ribosomal subunit protein ... , 2 types, 2 molecules qu

#12: Protein Small ribosomal subunit protein uS12


Mass: 14121.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsL, BKM63_03340, SAMN05444388_103390 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0C6
#16: Protein Small ribosomal subunit protein bS16


Mass: 20050.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsP, SAMN05444388_101644 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QGN9

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RNA chain , 1 types, 1 molecules 2

#22: RNA chain 16S rRNA


Mass: 491833.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria)

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Details

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: Ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431185 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00354081
ELECTRON MICROSCOPYf_angle_d0.57280406
ELECTRON MICROSCOPYf_dihedral_angle_d14.60120405
ELECTRON MICROSCOPYf_chiral_restr0.03610306
ELECTRON MICROSCOPYf_plane_restr0.0054640

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