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- PDB-9h90: Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit i... -

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Basic information

Entry
Database: PDB / ID: 9h90
TitleCryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.
Components
  • (30S ribosomal protein ...) x 16
  • 16S ribosomal RNA
  • Small ribosomal subunit protein uS7
KeywordsRIBOSOME / Vibrio natriegens / Bac5 / Bactenecin 5 / 50S / V. natriegens
Function / homology
Function and homology information


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 ...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 / cytosol / cytoplasm
Similarity search - Function
Type-1 KH domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type ...Type-1 KH domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, 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 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / 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 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. / 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 S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / : / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / K homology domain superfamily, prokaryotic type / 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 S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / S4 RNA-binding domain / S4 domain / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / RNA-binding S4 domain / Ribosomal protein S11 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9
Similarity search - Domain/homology
SPECTINOMYCIN / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS10 ...SPECTINOMYCIN / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5
Similarity search - Component
Biological speciesVibrio natriegens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRaulf, K.F. / Koller, T.O. / Beckert, B. / Morici, M. / Lepak, A. / Bange, G. / Wilson, D.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Other governmentDLR01Kl1820
German Research Foundation (DFG)SPP1879 (DFG WI3285/5-2) Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Authors: Karoline Raulf / Timm O Koller / Bertrand Beckert / Alexander Lepak / Martino Morici / Mario Mardirossian / Marco Scocchi / Gert Bange / Daniel N Wilson /
Abstract: Proline-rich antimicrobial peptides (PrAMPs) are produced as part of the innate immune response of animals, insects, and plants. The well-characterized mammalian PrAMP bactenecin-5 (Bac5) has been ...Proline-rich antimicrobial peptides (PrAMPs) are produced as part of the innate immune response of animals, insects, and plants. The well-characterized mammalian PrAMP bactenecin-5 (Bac5) has been shown to help fight bacterial infection by binding to the bacterial ribosome and inhibiting protein synthesis. In the absence of Bac5-ribosome structures, the binding mode of Bac5 and exact mechanism of action has remained unclear. Here, we present a cryo-electron microscopy structure of Bac5 in complex with the 70S ribosome from the Gram-negative marine bacterium Vibrio natriegens. The structure shows that, despite sequence similarity to Bac7 and other type I PrAMPs, Bac5 displays a completely distinct mode of interaction with the ribosomal exit tunnel. Bac5 overlaps with the binding site of both A- and P-site transfer RNAs bound at the peptidyltransferase center, suggesting that this type I PrAMP can interfere with late stages of translation initiation as well as early stages of elongation. Collectively, our study presents a ribosome structure from V. natriegens, a fast-growing bacterium that has interesting biotechnological and synthetic biology applications, as well as providing additional insights into the diverse binding modes that type I PrAMPs can utilize to inhibit protein synthesis.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
u: 30S ribosomal protein S21
C: 30S ribosomal protein S3
G: Small ribosomal subunit protein uS7
o: 30S ribosomal protein S15
h: 30S ribosomal protein S8
f: 30S ribosomal protein S6
e: 30S ribosomal protein S5
d: 30S ribosomal protein S4
I: 30S ribosomal protein S9
a: 16S ribosomal RNA
t: 30S ribosomal protein S20
r: 30S ribosomal protein S18
q: 30S ribosomal protein S17
p: 30S ribosomal protein S16
l: 30S ribosomal protein S12
k: 30S ribosomal protein S11
D: 30S ribosomal protein S14
J: 30S ribosomal protein S10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,53719
Polymers735,20418
Non-polymers3321
Water724
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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30S ribosomal protein ... , 16 types, 16 molecules uCohfedItrqplkDJ

#1: Protein 30S ribosomal protein S21


Mass: 8512.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUP2
#2: Protein 30S ribosomal protein S3


Mass: 25598.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y138
#4: Protein 30S ribosomal protein S15


Mass: 10084.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y3D6
#5: Protein 30S ribosomal protein S8


Mass: 14027.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0S4
#6: Protein 30S ribosomal protein S6


Mass: 14994.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y4F0
#7: Protein 30S ribosomal protein S5


Mass: 17609.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUS4
#8: Protein 30S ribosomal protein S4


Mass: 23392.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0XZY8
#9: Protein 30S ribosomal protein S9


Mass: 14638.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y103
#11: Protein 30S ribosomal protein S20


Mass: 9590.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUQ1
#12: Protein 30S ribosomal protein S18


Mass: 8861.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y440
#13: Protein 30S ribosomal protein S17


Mass: 9605.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0XZY2
#14: Protein 30S ribosomal protein S16


Mass: 9080.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y460
#15: Protein 30S ribosomal protein S12


Mass: 13738.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y4G9
#16: Protein 30S ribosomal protein S11


Mass: 13916.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y004
#17: Protein 30S ribosomal protein S14


Mass: 11481.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0L1
#18: Protein 30S ribosomal protein S10


Mass: 11741.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0R4

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Protein / RNA chain , 2 types, 2 molecules Ga

#10: RNA chain 16S ribosomal RNA


Mass: 500566.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria)
#3: Protein Small ribosomal subunit protein uS7


Mass: 17765.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y3T9

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Non-polymers , 2 types, 5 molecules

#19: Chemical ChemComp-SCM / SPECTINOMYCIN / ACTINOSPECTACIN / ESPECTINOMICINA / CHX-3101


Mass: 332.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N2O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Structure of the Vibrio natriegens 30S ribosomal subunit in complex with spectinomycin
Type: RIBOSOME / Entity ID: #1-#18 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio natriegens (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
29 mMMagnesium acetate1
35 mMPotassium phosphate1
495 mMPotassium glutamate1
55 mMAmmonium chloride1
60.5 mMCalcium chloride1
71 mMSpermidine1
88 mMPutrescine1
91 mMDithiothreitol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 8 OD/ml ribosome concentration
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 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 defocus max: 1200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0425 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294068 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementResolution: 2.8→233.42 Å / Cor.coef. Fo:Fc: 0.75 / SU B: 13.523 / SU ML: 0.238 / ESU R: 0.254
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.31811 --
obs0.31811 771735 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 64.992 Å2
Refinement stepCycle: 1 / Total: 47492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01151574
ELECTRON MICROSCOPYr_bond_other_d00.01730272
ELECTRON MICROSCOPYr_angle_refined_deg1.1091.84677103
ELECTRON MICROSCOPYr_angle_other_deg0.4191.73271382
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.52151903
ELECTRON MICROSCOPYr_dihedral_angle_2_deg11.3785192
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.98102922
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0510.29837
ELECTRON MICROSCOPYr_gen_planes_refined0.010.0236449
ELECTRON MICROSCOPYr_gen_planes_other0.0030.029383
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.2446.2657684
ELECTRON MICROSCOPYr_mcbond_other6.246.2637683
ELECTRON MICROSCOPYr_mcangle_it10.45911.249563
ELECTRON MICROSCOPYr_mcangle_other10.4611.2429564
ELECTRON MICROSCOPYr_scbond_it6.7946.46343890
ELECTRON MICROSCOPYr_scbond_other6.7936.46243890
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.45511.63667541
ELECTRON MICROSCOPYr_long_range_B_refined16.68367.7667687
ELECTRON MICROSCOPYr_long_range_B_other16.68467.7667688
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.756 57237 -
obs--100 %

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