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- EMDB-26311: Cryo-electron microscopy structure of human mt-SerRS in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-26311
TitleCryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(GCU-TL)
Map dataCryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(GCU-TL)
Sample
  • Complex: Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA
    • RNA: RNA (53-MER)
    • Protein or peptide: Serine--tRNA ligase, mitochondrial
  • Ligand: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
KeywordstRNA / SerRS / ligase-RNA complex / mitochondria / aminoacylation
Function / homology
Function and homology information


mitochondrial seryl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / ATP binding
Similarity search - Function
Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Serine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHirschi M / Kuhle B
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01GM125908 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG067594 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG061697 United States
National Institutes of Health/Office of the DirectorS10OD021634 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA.
Authors: Bernhard Kuhle / Marscha Hirschi / Lili K Doerfel / Gabriel C Lander / Paul Schimmel /
Abstract: Human mitochondrial gene expression relies on the specific recognition and aminoacylation of mitochondrial tRNAs (mtRNAs) by nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs). ...Human mitochondrial gene expression relies on the specific recognition and aminoacylation of mitochondrial tRNAs (mtRNAs) by nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs). Despite their essential role in cellular energy homeostasis, strong mutation pressure and genetic drift have led to an unparalleled sequence erosion of animal mtRNAs. The structural and functional consequences of this erosion are not understood. Here, we present cryo-EM structures of the human mitochondrial seryl-tRNA synthetase (mSerRS) in complex with mtRNA. These structures reveal a unique mechanism of substrate recognition and aminoacylation. The mtRNA is highly degenerated, having lost the entire D-arm, tertiary core, and stable L-shaped fold that define canonical tRNAs. Instead, mtRNA evolved unique structural innovations, including a radically altered T-arm topology that serves as critical identity determinant in an unusual shape-selective readout mechanism by mSerRS. Our results provide a molecular framework to understand the principles of mito-nuclear co-evolution and specialized mechanisms of tRNA recognition in mammalian mitochondrial gene expression.
History
DepositionFeb 23, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26311.png

Downloads & links

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Map

FileDownload / File: emd_26311.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(GCU-TL)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 168 pix.
= 193.2 Å		1.15 Å/pix.
x 168 pix.
= 193.2 Å		1.15 Å/pix.
x 168 pix.
= 193.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.049186926 - 0.07488911
Average (Standard dev.)0.000017854107 (±0.0026707994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 193.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA

EntireName: Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA
Components
  • Complex: Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA
    • RNA: RNA (53-MER)
    • Protein or peptide: Serine--tRNA ligase, mitochondrial
  • Ligand: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

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Supramolecule #1: Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA

SupramoleculeName: Human mt-SerRS in complex with mt-tRNA(GCU-TL) and SerSA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA (53-MER)

MacromoleculeName: RNA (53-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.884113 KDa
SequenceString:
GAGAAAGCUC ACAAGGCCAU GCCCCCAUGU CUAACAACAU GGCUUUCUCA CCA

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Macromolecule #2: Serine--tRNA ligase, mitochondrial

MacromoleculeName: Serine--tRNA ligase, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine-tRNA ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.358391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAASMARRLW PLLTRRGFRP RGGCISNDSP RRSFTTEKRN RNLLYEYARE GYSALPQLDI ERFCACPEEA AHALELRKGE LRSADLPAI ISTWQELRQL QEQIRSLEEE KAAVTEAVRA LLANQDSGEV QQDPKYQGLR ARGREIRKEL VHLYPREAQL E EQFYLQAL ...String:
MAASMARRLW PLLTRRGFRP RGGCISNDSP RRSFTTEKRN RNLLYEYARE GYSALPQLDI ERFCACPEEA AHALELRKGE LRSADLPAI ISTWQELRQL QEQIRSLEEE KAAVTEAVRA LLANQDSGEV QQDPKYQGLR ARGREIRKEL VHLYPREAQL E EQFYLQAL KLPNQTHPDV PVGDESQARV LHMVGDKPVF SFQPRGHLEI GEKLDIIRQK RLSHVSGHRS YYLRGAGALL QH GLVNFTF NKLLRRGFTP MTVPDLLRGA VFEGCGMTPN ANPSQIYNID PARFKDLNLA GTAEVGLAGY FMDHTVAFRD LPV RMVCSS TCYRAETNTG QEPRGLYRVH HFTKVEMFGV TGPGLEQSSQ LLEEFLSLQM EILTELGLHF RVLDMPTQEL GLPA YRKFD IEAWMPGRGR FGEVTSASNC TDFQSRRLHI MFQTEAGELQ FAHTVNATAC AVPRLLIALL ESNQQKDGSV LVPPA LQSY LGTDRITAPT HVPLQYIGPN QPRKPGLPGQ PAVS

UniProtKB: Serine--tRNA ligase, mitochondrial

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Macromolecule #3: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

MacromoleculeName: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: SSA
Molecular weightTheoretical: 433.397 Da
Chemical component information

ChemComp-SSA:
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118269
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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