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- PDB-9h91: Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit i... -

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Basic information

Entry
Database: PDB / ID: 9h91
TitleCryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Components
  • (50S ribosomal protein ...) x 26
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Cathelicidin-2
  • Large ribosomal subunit protein bL9
KeywordsRIBOSOME / Vibrio natriegens / Bac5 / Bactenecin 5 / 50S / V. natriegens
Function / homology
Function and homology information


assembly of large subunit precursor of preribosome / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium ...assembly of large subunit precursor of preribosome / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / defense response to Gram-positive bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / innate immune response / mRNA binding / extracellular space / cytoplasm
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / : / : / Cystatin superfamily / Ribosomal protein L25, short-form / Ribosomal protein L16 signature 1. ...Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / : / : / Cystatin superfamily / Ribosomal protein L25, short-form / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL16 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL19 / Cathelicidin-2
Similarity search - Component
Biological speciesVibrio natriegens (bacteria)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
9: Cathelicidin-2
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
G: 50S ribosomal protein L6
H: Large ribosomal subunit protein bL9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
A: 23S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,55331
Polymers1,263,48830
Non-polymers651
Water32418
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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50S ribosomal protein ... , 26 types, 26 molecules 01234CDEGJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L32


Mass: 6314.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y2T2
#2: Protein 50S ribosomal protein L33


Mass: 6540.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0XZW0
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5198.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y4Q5
#4: Protein 50S ribosomal protein L35


Mass: 7324.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y2A7
#5: Protein/peptide 50S ribosomal protein L36


Mass: 4291.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y149
#8: Protein 50S ribosomal protein L2


Mass: 30059.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUJ7
#9: Protein 50S ribosomal protein L3


Mass: 22393.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUL8
#10: Protein 50S ribosomal protein L4


Mass: 21906.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CVG6
#11: Protein 50S ribosomal protein L6


Mass: 18801.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUM2
#13: Protein 50S ribosomal protein L13


Mass: 15990.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0U3
#14: Protein 50S ribosomal protein L14


Mass: 13594.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0F6
#15: Protein 50S ribosomal protein L15


Mass: 14878.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUX1
#16: Protein 50S ribosomal protein L16


Mass: 15557.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0C5
#17: Protein 50S ribosomal protein L17


Mass: 14231.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y071
#18: Protein 50S ribosomal protein L18


Mass: 12641.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CVH0
#19: Protein 50S ribosomal protein L19


Mass: 13305.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CWW0
#20: Protein 50S ribosomal protein L20


Mass: 13414.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CVB0
#21: Protein 50S ribosomal protein L21


Mass: 11544.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CVI2
#22: Protein 50S ribosomal protein L22


Mass: 12181.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y0L0
#23: Protein 50S ribosomal protein L23


Mass: 11151.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUR9
#24: Protein 50S ribosomal protein L24


Mass: 11239.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y061
#25: Protein 50S ribosomal protein L25


Mass: 10391.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y4S6
#26: Protein 50S ribosomal protein L27


Mass: 9228.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUT7
#27: Protein 50S ribosomal protein L28


Mass: 9056.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y076
#28: Protein 50S ribosomal protein L29


Mass: 7205.347 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0XZZ8
#29: Protein 50S ribosomal protein L30


Mass: 6596.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN1CUK2

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RNA chain , 2 types, 2 molecules BA

#7: RNA chain 5S ribosomal RNA


Mass: 38990.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria)
#30: RNA chain 23S ribosomal RNA


Mass: 881521.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria)

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Protein/peptide / Protein , 2 types, 2 molecules 9H

#12: Protein Large ribosomal subunit protein bL9


Mass: 15769.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio natriegens (bacteria) / References: UniProt: A0AAN0Y4G6
#6: Protein/peptide Cathelicidin-2 / Bactenecin-5 / Bac5 / PR-42 / Bactenecin-5 (1-17) / Bac5 (1-17).


Mass: 2167.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bactenecin-5 (1-17) / Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P19660

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Non-polymers , 2 types, 19 molecules

#31: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: Structure of the Proline-rich Antimicrobial Peptide Bac5(1-17) in Complex with the Vibrio natriegens 50S ribosomal subunit
Type: RIBOSOME / Entity ID: #1-#30 / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294068 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementResolution: 2.7→224.93 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 5.145 / SU ML: 0.103 / ESU R: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.20425 --
obs0.20425 982854 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 93.352 Å2
Refinement stepCycle: 1 / Total: 83761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01191333
ELECTRON MICROSCOPYr_bond_other_d0.0010.01851486
ELECTRON MICROSCOPYr_angle_refined_deg1.4221.846137328
ELECTRON MICROSCOPYr_angle_other_deg0.5411.725121844
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.81952914
ELECTRON MICROSCOPYr_dihedral_angle_2_deg12.2975274
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.729104482
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0630.217663
ELECTRON MICROSCOPYr_gen_planes_refined0.0160.0261642
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0216218
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_it12.5568.96911743
ELECTRON MICROSCOPYr_mcbond_other12.5568.96811743
ELECTRON MICROSCOPYr_mcangle_it15.70516.22814628
ELECTRON MICROSCOPYr_mcangle_other15.70716.22914629
ELECTRON MICROSCOPYr_scbond_it12.6879.43579590
ELECTRON MICROSCOPYr_scbond_other12.6879.43579591
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.66317.109122701
ELECTRON MICROSCOPYr_long_range_B_refined19.555106.66122607
ELECTRON MICROSCOPYr_long_range_B_other19.555106.66122606
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.626 72752 -
obs--100 %

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