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- PDB-9pyc: Cryo-EM structure of EF-G and RaiA simultaneously bound to an E. ... -

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Basic information

Entry
Database: PDB / ID: 9pyc
TitleCryo-EM structure of EF-G and RaiA simultaneously bound to an E. coli ribosome imaged in a cell lysate
Components
  • Elongation factor G
  • Ribosome-associated inhibitor A
KeywordsRIBOSOMAL PROTEIN / hibernation / elongation factor / bacterial ribosome
Function / homology
Function and homology information


dormancy process / negative regulation of translational elongation / ribosome disassembly / guanosine tetraphosphate binding / ribosomal small subunit binding / translational elongation / translation elongation factor activity / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit ...dormancy process / negative regulation of translational elongation / ribosome disassembly / guanosine tetraphosphate binding / ribosomal small subunit binding / translational elongation / translation elongation factor activity / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / rRNA binding / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III ...: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor G / Ribosome-associated inhibitor A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMay, M.B. / Davis, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-CAREER grant 2046778 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM144542 United States
CitationJournal: To Be Published
Title: Capturing ribosomal structures in cellular extracts with cryoPRISM: A purification-free cryoEM approach reveals novel structural states
Authors: May, M.B. / Lopez-Perez, G.S. / Davis, J.H.
History
DepositionAug 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 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: Elongation factor G
F: Ribosome-associated inhibitor A


Theoretical massNumber of molelcules
Total (without water)90,4802
Polymers90,4802
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

#1: Protein Elongation factor G / EF-G


Mass: 77676.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: NCM3722
References: UniProt: P0A6M8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein Ribosome-associated inhibitor A / Protein Y / pY / Ribosome associated factor Y / Spot Y


Mass: 12803.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: NCM3722 / References: UniProt: P0AD49
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: Crude cell extract / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Frozen cell pellets were lysed under cryogenic conditions using a cryomill. Frozen lysate was resuspended and clarified via centrifugation at 21,000g. DNase I (33 U/mL) was added and crude ...Details: Frozen cell pellets were lysed under cryogenic conditions using a cryomill. Frozen lysate was resuspended and clarified via centrifugation at 21,000g. DNase I (33 U/mL) was added and crude cell extract was plunge-frozen.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: NCM3722
Buffer solutionpH: 7.5
Details: 33 U/mL DNase I (New England Biolabs #M0303L) was added in addition.
Buffer component
IDConc.NameFormulaBuffer-ID
128 mMTris(hydroxymethyl)aminomethane hydrochloride pH 7.5C4H13Cl2NO1
290 mMAmmonium chlorideNH4Cl1
30.45 mMEthylenediaminetetraacetic AcidC10H16N2O81
45.4 mM2-MercaptoethanolC2H6OS1
50.5 mMCalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grid was coated with monolayer graphene following (Grassetti et al, JOVE 2023) and treated with UV/ozone for 10 minutes using a Bioforce PC440 UV/ozone cleaner
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 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: 2000 nm / Nominal defocus min: 30 nm
Image recordingElectron dose: 45.1838 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
4Warp1.0.9CTF correction
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoDRGN2.2classification
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
14PHENIX1.21.2-5419model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1503396
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21018 / Symmetry type: POINT

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