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- EMDB-26632: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-26632
TitleCompact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)
Map data
Sample
  • Complex: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)
    • Protein or peptide: Translation initiation factor IF-2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsInitiation Factor 2 / 70S ribosome / cryo-EM / translation initiation / initiator tRNA / conformational changes / RIBOSOME
Function / homology
Function and homology information


translational initiation / translation initiation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Putative DNA-binding domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Translation initiation factor IF-2
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBasu RS / Sherman MB / Gagnon MG
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136936 United States
Robert A. Welch FoundationH-2032-20200401 United States
CitationJournal: Nat Commun / Year: 2022
Title: Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation
Authors: Basu RS / Sherman MB / Gagnon MG
History
DepositionApr 11, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26632.png

Downloads & links

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Map

FileDownload / File: emd_26632.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.78250086 - 1.6576998
Average (Standard dev.)-0.0063980967 (±0.02432006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26632_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...

Fileemd_26632_additional_1.map
AnnotationCompact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-B). Sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...

Fileemd_26632_half_map_1.map
AnnotationCompact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-B). Half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S...

Fileemd_26632_half_map_2.map
AnnotationCompact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex (I-B). Half-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 : Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ...

EntireName: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)
Components
  • Complex: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)
    • Protein or peptide: Translation initiation factor IF-2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome ...

SupramoleculeName: Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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Macromolecule #1: Translation initiation factor IF-2

MacromoleculeName: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 91.049641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQVTVKELA QVVDTPVERL LLQMRDAGLP HTSAEQVVTD SEKQALLTHL KGSHGDRASE PRKITLQRKT TTTLKVGGSK TVSVEVRKK KTYVKRSPDE IEAERQRELE EQRAAEEAER LKAEEAAARQ RAEEEARKAE EAARAKAAQE AAATAGAEPA V VADVAVAE ...String:
MTQVTVKELA QVVDTPVERL LLQMRDAGLP HTSAEQVVTD SEKQALLTHL KGSHGDRASE PRKITLQRKT TTTLKVGGSK TVSVEVRKK KTYVKRSPDE IEAERQRELE EQRAAEEAER LKAEEAAARQ RAEEEARKAE EAARAKAAQE AAATAGAEPA V VADVAVAE PVAKPAAVEE RKKEEPRRVP KRDEDDDRRD RKHTQHRPSV KEKEKVPAPR VAPRSTDEES DGYRRGGRGG KS KLKKRNQ HGFQNPTGPI VREVNIGETI TVAELAAQMS VKGAEVVKFM FKMGSPVTIN QVLDQETAQL VAEELGHKVK LVS ENALEE QLAESLKFEG EAVTRAPVVT VMGHVDHGKT SLLDYIRRAK VAAGEAGGIT QHIGAYHVET ERGMVTFLDT PGHA AFTAM RARGAQATDI VILVVAADDG VMPQTQEAVQ HAKAAGVPIV VAVNKIDKPE ANPDNIKNGL AALDVIPEEW GGDAP FVPV SAKLGTGVDE LLEAVLLQAE VLELKATPSA PGRGVVVESR LDKGRGPVAT VLVQDGTLRQ GDMVLVGINY GRVRAM LDE NGKPIKEAGP SIPVEILGLD GTPDAGDEMT VVADEKKARE VALFRQGKFR EVKLARAHAG KLENIFENMG QEEKKTL NI VLKADVRGSL EALQGSLSGL GNDEVQVRVV GGGVGGITES DANLALASNA VLFGFNVRAD AGARKIVEAE GLDMRYYN V IYDIIEDVKK ALTGMLGSDL RENILGIAEV RDVFRSPKFG AIAGCMVTEG MVHRNRPIRV LRDDVVIFEG ELESLRRFK DDVAEVRAGM ECGIGVKSYN DVKVGDKIEV FEKVEVARSL

UniProtKB: Translation initiation factor IF-2

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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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: 7.6
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8056 / Average exposure time: 1.0 sec. / Average electron dose: 31.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 878576
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 24614

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Atomic model buiding 1

Initial modelPDB ID:

3jcj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7unt:
Compact IF2-GDP bound to the Pseudomonas aeruginosa 70S ribosome initiation complex, from focused classification and refinement (I-B)

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