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- EMDB-33240: Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33240
TitleCryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (both in tRNA binding states)
Map data
Sample
  • Complex: complex
    • Complex: glycyl-tRNA synthetaseGlycine—tRNA ligase
      • Protein or peptide: Glycine--tRNA ligase
    • Complex: tRNATransfer RNA
      • RNA: tRNA(gly)
Function / homology
Function and homology information


arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / embryo development ending in seed dormancy / regulation of embryonic development / chloroplast / mitochondrion / ATP binding
Similarity search - Function
Glycine-tRNA ligase, beta subunit / Glycyl-tRNA synthetase beta subunit / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / DALR anticodon binding / DALR anticodon binding domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
glycine--tRNA ligase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice) / Oryza sativa (Asian cultivated rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYu Z / Wu Z / Li Y / Lu G / Lin J
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770784 China
National Natural Science Foundation of China (NSFC)31802147 China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structural basis of a two-step tRNA recognition mechanism for plastid glycyl-tRNA synthetase.
Authors: Zhaoli Yu / Zihan Wu / Ye Li / Qiang Hao / Xiaofeng Cao / Gregor M Blaha / Jinzhong Lin / Guoliang Lu /
Abstract: Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some ...Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some bacteria, the α and β subunits are fused and are designated as (αβ)2 GlyRSs. While the tRNA recognition and aminoacylation mechanisms are well understood for α2 GlyRSs, little is known about the mechanisms for α2β2/(αβ)2 GlyRSs. Here we describe structures of the (αβ)2 GlyRS from Oryza sativa chloroplast by itself and in complex with cognate tRNAGly. The set of structures reveals that the U-shaped β half of the synthetase selects the tRNA in a two-step manner. In the first step, the synthetase engages the elbow and the anticodon base C35 of the tRNA. In the second step, the tRNA has rotated ∼9° toward the catalytic centre. The synthetase probes the tRNA for the presence of anticodon base C36 and discriminator base C73. This intricate mechanism enables the tRNA to access the active site of the synthetase from a direction opposite to that of most other class II synthetases.
History
DepositionApr 19, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33240.png

Downloads & links

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Map

FileDownload / File: emd_33240.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.16023304 - 0.23069122
Average (Standard dev.)-1.12514035e-05 (±0.0029093926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33240_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33240_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_33240_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 : complex

EntireName: complex
Components
  • Complex: complex
    • Complex: glycyl-tRNA synthetaseGlycine—tRNA ligase
      • Protein or peptide: Glycine--tRNA ligase
    • Complex: tRNATransfer RNA
      • RNA: tRNA(gly)

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Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all

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Supramolecule #2: glycyl-tRNA synthetase

SupramoleculeName: glycyl-tRNA synthetase / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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Supramolecule #3: tRNA

SupramoleculeName: tRNA / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: Glycine--tRNA ligase

MacromoleculeName: Glycine--tRNA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine-tRNA ligase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 117.050477 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHHHGS SLEVLFQGPA VASADGDAPS PVSVSASAAT KGPSSSSVLT FQQAIQRLQD YWASVGCAVM QCSNTEVGAG TMNPLTFLR VLGPEPWNVA YVEPSIRPDD SRYGDNPNRL QRHTQFQVIL KPDPGNSQDL FLHSLSALGI NVREHDIRFV E DNWESPVL ...String:
HHHHHHHHGS SLEVLFQGPA VASADGDAPS PVSVSASAAT KGPSSSSVLT FQQAIQRLQD YWASVGCAVM QCSNTEVGAG TMNPLTFLR VLGPEPWNVA YVEPSIRPDD SRYGDNPNRL QRHTQFQVIL KPDPGNSQDL FLHSLSALGI NVREHDIRFV E DNWESPVL GAWGLGWEVW MDGMEITQFT YFQQSGSLPL LPVSVEITYG LERILMSLQG VDHFKNIQYT KGITYGELFL EN EKEMSAY YLEHANVDNI QKHFDDFEEE ARSLLSLWLP IPAYDHVLKA SHAFNILDSR GFVGVTERAR YFGRMRSLAR QCA QLWVKT RENLGYPLGT YQESNLIYPH VSEKPSRKGV VGQPRAFVLE IGTEELPPHD VIEATKQLEK SLIQILEKRR LSHG KVRSY GTPRRLAVVV ENLNMKQMEE EIELRGPPVA KAFDQEGRPT KAAEGFCRKN NVPIDSLYRR TDGKTEYIYA RVKES ARFA DEVLTEDLPT IISGISFPKS MRWNSNIVFS RPIRWIFALH GDLIVPFCFA GISSGNQSCG LRNSSLANFK VEAAEL YLH TLEKAGILID MQERKQRILH DSSILAEGVG GDIIAPDSLV QEVINLVEAP MPIIGRYDVS FLALPKDVLI TVMQKHQ KY FPVTSKTMGN LLPCFITVAN GAIKEEVVRK GNEAVLRARY EDAKFFYKMD TQKKLSEFRD QLSSILFHER LGTMLDKM K RVENTVAEVA LLLGINEKMI PAIKDAAALA MSDLATNIVT EFTSLAGIMA RHYALRDGLS EQIAEALFEI TLPRFSGDV FPKTDPGIVL AVTDRLDSLV GLFGAGCQPS STNDPFGLRR ISYGLVQILV ENKKNFDLTK ALTLVAEEQP ITIDSGVIDE VVQFVTRRL EQLLVDEGIN CEIVRSVLIE RANCPYLASQ TAIEMEAFSR TEDFPKIVEA YSRPTRIIRG KEIGSALEVD A SVFEKDEE RALWSAYLEV ADKIHPGVDI KAFADASLEL LQPLEDFFTN VFVMAEDEKV RNNRLALLTK VASLPKGIAD LS VLPGF

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Macromolecule #2: tRNA(gly)

MacromoleculeName: tRNA(gly) / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Molecular weightTheoretical: 23.906104 KDa
SequenceString:
(GTP)CGAGCGUAG UUCAAUGGUA AAACAUCUCC UUGCCAAGGA GAAGAUACGG GUUCGAUUCC CGCCGCUCGC CCCA

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32038
FSC plot (resolution estimation)

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