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- EMDB-29070: Cryo-electron microscopy structure of human mt-SerRS in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-29070
TitleCryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(UGA-TL)
Map data
Sample
  • Complex: Human mt-SerRS in complex with mt-tRNA(UGA-TL) and SerSA
    • Protein or peptide: Serine--tRNA ligase, mitochondrial
    • RNA: mt-tRNA(UGA-TL)
  • Ligand: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
KeywordstRNA / SerRS / transcription / ligase-RNA complex
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 / cytosol
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: 3.6 Å
AuthorsHirschi M / Kuhle B / Doerfel L / Schimmel P / Lander G
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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: 2023
Title: Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition.
Authors: Bernhard Kuhle / Marscha Hirschi / Lili K Doerfel / Gabriel C Lander / Paul Schimmel /
Abstract: Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic ...Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNA isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNA, and perform a structural and functional comparison with the mSerRS-mtRNA complex. We find that despite their common function, mtRNA and mtRNA show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNA. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.
History
DepositionDec 11, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29070.png

Downloads & links

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Map

FileDownload / File: emd_29070.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 192 pix.
= 220.8 Å		1.15 Å/pix.
x 192 pix.
= 220.8 Å		1.15 Å/pix.
x 192 pix.
= 220.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.21106106 - 0.312332
Average (Standard dev.)0.000006627178 (±0.010662936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 220.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29070_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29070_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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

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

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

SupramoleculeName: Human mt-SerRS in complex with mt-tRNA(UGA-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: Serine--tRNA ligase, mitochondrial

MacromoleculeName: Serine--tRNA ligase, mitochondrial / type: protein_or_peptide / ID: 1 / 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 #2: mt-tRNA(UGA-TL)

MacromoleculeName: mt-tRNA(UGA-TL) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.41141 KDa
SequenceString:
GAAAAAGUCA UGGAGGCCAU GGGGUCC(N)(N)(N) (N)(N)(N)(N)(N)(N)GGGC UUUGGGGGGU UCGAUUCCUU CC UUUUUUG C

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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
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3448 / Average exposure time: 11.8 sec. / 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

Particle selectionNumber selected: 7218136
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tzb

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 881655
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8ffy:
Cryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(UGA-TL)

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