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- PDB-8uua: Cryo-EM structure of the Listeria innocua 50S ribosomal subunit i... -

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Basic information

Entry
Database: PDB / ID: 8uua
TitleCryo-EM structure of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)
Components
  • (Large ribosomal subunit protein ...) x 27
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • GTPase HflX
KeywordsRIBOSOME / cryo-EM / recycling / HflXr / time-resolved
Function / homology
Function and homology information


large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation ...large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 type B / : ...GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 type B / : / : / 50S ribosome-binding GTPase / GTP binding domain / : / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / : / 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 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 L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / 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 L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature.
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL23 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19 / GTPase HflX
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
Listeria innocua (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSeely, S.M. / Basu, R.S. / Gagnon, M.G.
Funding support United States, 4items
OrganizationGrant numberCountry
Other governmentUniversity of Texas Medical Branch
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136936 United States
Welch FoundationH-2032-20230405 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008280 United States
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Mechanistic insights into the alternative ribosome recycling by HflXr.
Authors: Savannah M Seely / Ritwika S Basu / Matthieu G Gagnon /
Abstract: During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue ...During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
v: GTPase HflX
A: 23S Ribosomal RNA
B: 5S Ribosomal RNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
L: Large ribosomal subunit protein uL13
M: Large ribosomal subunit protein uL14
N: Large ribosomal subunit protein uL15
O: Large ribosomal subunit protein uL16
P: Large ribosomal subunit protein bL17
Q: Large ribosomal subunit protein uL18
R: Large ribosomal subunit protein bL19
S: Large ribosomal subunit protein bL20
T: Large ribosomal subunit protein bL21
U: Large ribosomal subunit protein uL22
V: Large ribosomal subunit protein uL23
W: Large ribosomal subunit protein uL24
Y: Large ribosomal subunit protein bL27
Z: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
2: Large ribosomal subunit protein uL30
3: Large ribosomal subunit protein bL31B
4: Large ribosomal subunit protein bL32
5: Large ribosomal subunit protein bL33
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: Large ribosomal subunit protein bL36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,390,789235
Polymers1,385,17130
Non-polymers5,618205
Water2,414134
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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Protein , 1 types, 1 molecules v

#1: Protein GTPase HflX / GTP-binding protein HflX


Mass: 47610.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / References: UniProt: Q8Y8Y0

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RNA chain , 2 types, 2 molecules AB

#2: RNA chain 23S Ribosomal RNA


Mass: 951061.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 2288068686
#3: RNA chain 5S Ribosomal RNA


Mass: 37304.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 1774324476

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Large ribosomal subunit protein ... , 27 types, 27 molecules CDEFGLMNOPQRSTUVWYZ12345678

#4: Protein Large ribosomal subunit protein uL2


Mass: 30568.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A742
#5: Protein Large ribosomal subunit protein uL3


Mass: 22880.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ADD0
#6: Protein Large ribosomal subunit protein uL4


Mass: 22640.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSH7
#7: Protein Large ribosomal subunit protein uL5


Mass: 20023.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AWX6
#8: Protein Large ribosomal subunit protein uL6


Mass: 19433.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ALU0
#9: Protein Large ribosomal subunit protein uL13


Mass: 16228.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AGN0
#10: Protein Large ribosomal subunit protein uL14


Mass: 13248.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AP82
#11: Protein Large ribosomal subunit protein uL15


Mass: 15827.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5A6S7
#12: Protein Large ribosomal subunit protein uL16


Mass: 16171.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSU8
#13: Protein Large ribosomal subunit protein bL17


Mass: 15237.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSW3
#14: Protein Large ribosomal subunit protein uL18


Mass: 13107.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AR65
#15: Protein Large ribosomal subunit protein bL19


Mass: 13089.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A6B0JQF2
#16: Protein Large ribosomal subunit protein bL20


Mass: 13719.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JH71
#17: Protein Large ribosomal subunit protein bL21


Mass: 11220.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AD18
#18: Protein Large ribosomal subunit protein uL22


Mass: 12895.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5ANW2
#19: Protein Large ribosomal subunit protein uL23


Mass: 10949.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4MTC5
#20: Protein Large ribosomal subunit protein uL24


Mass: 11219.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AD05
#21: Protein Large ribosomal subunit protein bL27


Mass: 10571.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JMC7
#22: Protein Large ribosomal subunit protein bL28


Mass: 7010.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JJV9
#23: Protein Large ribosomal subunit protein uL29


Mass: 7414.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AGL9
#24: Protein Large ribosomal subunit protein uL30


Mass: 6504.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4VSJ1
#25: Protein Large ribosomal subunit protein bL31B


Mass: 9274.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U4MT39
#26: Protein Large ribosomal subunit protein bL32


Mass: 6534.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JNN0
#27: Protein/peptide Large ribosomal subunit protein bL33


Mass: 6021.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JRA4
#28: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5319.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JKZ6
#29: Protein Large ribosomal subunit protein bL35


Mass: 7746.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A660JIB9
#30: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4336.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: UniProt: A0A0U5AM58

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Non-polymers , 5 types, 339 molecules

#31: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 200 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#35: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: Listeria innocua 50S ribosomal subunit bound to HflXr / Type: RIBOSOME / Entity ID: #1-#19, #21-#30 / Source: NATURAL
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Listeria innocua (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 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: 96000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10446

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
2SerialEMimage acquisition
3cryoSPARC4.1.2masking
4cryoSPARC4.1.2CTF correction
7UCSF Chimera1.14model fitting
8PHENIX1.19.2.4158model refinement
10cryoSPARC4.1.2initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12cryoSPARC4.1.2classification
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332513 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7NHN

7nhn


Accession code: 7NHN / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00798801
ELECTRON MICROSCOPYf_angle_d0.72148366
ELECTRON MICROSCOPYf_dihedral_angle_d14.20839824
ELECTRON MICROSCOPYf_chiral_restr0.04719071
ELECTRON MICROSCOPYf_plane_restr0.0077571

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