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- EMDB-72030: Cryo-EM structure of EF-G and RaiA simultaneously bound to an E. ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72030
TitleCryo-EM structure of EF-G and RaiA simultaneously bound to an E. coli ribosome imaged in a cell lysate
Map dataThis EM map is for the entire ribosome, EF-G and RaiA were built into a portion of this map.
Sample
  • Organelle or cellular component: Crude cell extract
    • Protein or peptide: Elongation factor G
    • Protein or peptide: Ribosome-associated inhibitor A
Keywordshibernation / elongation factor / bacterial ribosome / RIBOSOMAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMay MB / Davis JH
Funding support United States, 2 items
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 MB / Lopez-Perez GS / Davis JH
History
DepositionAug 7, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72030.png

Downloads & links

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Map

FileDownload / File: emd_72030.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis EM map is for the entire ribosome, EF-G and RaiA were built into a portion of this map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.5860195 - 1.639197
Average (Standard dev.)0.0020695364 (±0.066883385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 466.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72030_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72030_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72030_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Crude cell extract

EntireName: Crude cell extract
Components
  • Organelle or cellular component: Crude cell extract
    • Protein or peptide: Elongation factor G
    • Protein or peptide: Ribosome-associated inhibitor A

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Supramolecule #1: Crude cell extract

SupramoleculeName: Crude cell extract / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
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.
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: NCM3722

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Macromolecule #1: Elongation factor G

MacromoleculeName: Elongation factor G / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: NCM3722
Molecular weightTheoretical: 77.676227 KDa
SequenceString: MARTTPIARY RNIGISAHID AGKTTTTERI LFYTGVNHKI GEVHDGAATM DWMEQEQERG ITITSAATTA FWSGMAKQYE PHRINIIDT PGHVDFTIEV ERSMRVLDGA VMVYCAVGGV QPQSETVWRQ ANKYKVPRIA FVNKMDRMGA NFLKVVNQIK T RLGANPVP ...String:
MARTTPIARY RNIGISAHID AGKTTTTERI LFYTGVNHKI GEVHDGAATM DWMEQEQERG ITITSAATTA FWSGMAKQYE PHRINIIDT PGHVDFTIEV ERSMRVLDGA VMVYCAVGGV QPQSETVWRQ ANKYKVPRIA FVNKMDRMGA NFLKVVNQIK T RLGANPVP LQLAIGAEEH FTGVVDLVKM KAINWNDADQ GVTFEYEDIP ADMVELANEW HQNLIESAAE ASEELMEKYL GG EELTEAE IKGALRQRVL NNEIILVTCG SAFKNKGVQA MLDAVIDYLP SPVDVPAING ILDDGKDTPA ERHASDDEPF SAL AFKIAT DPFVGNLTFF RVYSGVVNSG DTVLNSVKAA RERFGRIVQM HANKREEIKE VRAGDIAAAI GLKDVTTGDT LCDP DAPII LERMEFPEPV ISIAVEPKTK ADQEKMGLAL GRLAKEDPSF RVWTDEESNQ TIIAGMGELH LDIIVDRMKR EFNVE ANVG KPQVAYRETI RQKVTDVEGK HAKQSGGRGQ YGHVVIDMYP LEPGSNPKGY EFINDIKGGV IPGEYIPAVD KGIQEQ LKA GPLAGYPVVD MGIRLHFGSY HDVDSSELAF KLAASIAFKE GFKKAKPVLL EPIMKVEVET PEENTGDVIG DLSRRRG ML KGQESEVTGV KIHAEVPLSE MFGYATQLRS LTKGRASYTM EFLKYDEAPS NVAQAVIEAR GK

UniProtKB: Elongation factor G

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Macromolecule #2: Ribosome-associated inhibitor A

MacromoleculeName: Ribosome-associated inhibitor A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: NCM3722
Molecular weightTheoretical: 12.803583 KDa
SequenceString:
MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA DATINTPNGV LVASGKHEDM YTAINELINK LERQLNKLQ HKGEARRAAT SVKDANFVEE VEEE

UniProtKB: Ribosome-associated inhibitor A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
28.0 mMC4H13Cl2NOTris(hydroxymethyl)aminomethane hydrochloride pH 7.5
90.0 mMNH4ClAmmonium chloride
0.45 mMC10H16N2O8Ethylenediaminetetraacetic Acid
5.4 mMC2H6OS2-Mercaptoethanol
0.5 mMCaCl2Calcium chloride

Details: 33 U/mL DNase I (New England Biolabs #M0303L) was added in addition.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS
Details: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.1838 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.03 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1503396
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 21018
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware: (Name: cryoDRGN (ver. 2.2), cryoSPARC (ver. 4.5.3))
FSC plot (resolution estimation)

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