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- PDB-7tzb: Crystal structure of the human mitochondrial seryl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 7tzb
TitleCrystal structure of the human mitochondrial seryl-tRNA synthetase (mt SerRS) bound with a seryl-adenylate analogue
ComponentsSerine--tRNA ligase, mitochondrial
KeywordsLIGASE / Seryl-tRNA synthetase / mitochondria / aminoacylation / translation / tRNA / class II / alpha-beta domain
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
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsKuhle, B. / Hirschi, M. / Doerfel, L. / Lander, G. / Schimmel, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM125908-01A1 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 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine--tRNA ligase, mitochondrial
B: Serine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7624
Polymers108,8962
Non-polymers8672
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-31 kcal/mol
Surface area40490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.590, 150.590, 142.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 39 through 278 or resid 280 through 334 or resid 339 through 506))
21(chain B and (resid 39 through 122 or (resid 123...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 39 through 278 or resid 280 through 334 or resid 339 through 506))A39 - 278
121(chain A and (resid 39 through 278 or resid 280 through 334 or resid 339 through 506))A280 - 334
131(chain A and (resid 39 through 278 or resid 280 through 334 or resid 339 through 506))A339 - 506
211(chain B and (resid 39 through 122 or (resid 123...B39 - 122
221(chain B and (resid 39 through 122 or (resid 123...B123 - 125
231(chain B and (resid 39 through 122 or (resid 123...B39 - 506
241(chain B and (resid 39 through 122 or (resid 123...B39 - 506
251(chain B and (resid 39 through 122 or (resid 123...B39 - 506
261(chain B and (resid 39 through 122 or (resid 123...B39 - 506

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Components

#1: Protein Serine--tRNA ligase, mitochondrial / SerRSmt / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 54447.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS2, SARSM / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NP81, serine-tRNA ligase
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 9 / Details: 0.1 M Bicine, 10 mM Spermidine, 8% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→37.65 Å / Num. obs: 23497 / % possible obs: 92.4 % / Redundancy: 5.082 % / Biso Wilson estimate: 98.344 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.064 / Χ2: 1.083 / Net I/σ(I): 15.44 / Num. measured all: 119402 / Scaling rejects: 2755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.024.9571.0821.639280187818720.7591.21199.7
3.02-3.114.8470.6442.538899185318360.890.72399.1
3.11-3.25.4280.4833.569733179317930.940.535100
3.2-3.35.4020.4054.289242171317110.9520.44999.9
3.3-3.45.2280.3015.388176170015640.9730.33692
3.4-3.524.4370.2019.655591159412600.970.22979
3.52-3.665.050.2457.196515157912900.9810.27481.7
3.66-3.814.5210.159.874684148710360.9870.1769.7
3.81-3.984.990.11313.28433114748680.9940.12658.9
3.98-4.175.3610.06919.167291136013600.9970.077100
4.17-4.395.3220.05922.936961131313080.9980.06599.6
4.39-4.665.1670.0526.286443125112470.9970.05699.7
4.66-4.984.7460.04727.035477117011540.9980.05398.6
4.98-5.385.2410.04628.455686108810850.9980.05199.7
5.38-5.95.3340.04329.7552869929910.9980.04799.9
5.9-6.595.2080.04230.7746829068990.9980.04699.2
6.59-7.614.6850.03732.8736268027740.9980.04196.5
7.61-9.325.3050.03338.1835496736690.9990.03799.4
9.32-13.185.0830.03139.2525775155070.9990.03498.4
13.18-37.655.0290.03239.5913732902730.9990.03694.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.8 Å37.65 Å
Translation6.8 Å37.65 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.5.7phasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1WLE

1wle


Resolution: 2.95→37.65 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 36.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 1172 5 %
Rwork0.2374 22273 -
obs0.2398 23445 92.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 274.06 Å2 / Biso mean: 123.656 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.95→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 0 58 0 7382
Biso mean--100.12 --
Num. residues----924
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2816X-RAY DIFFRACTION9.274TORSIONAL
12B2816X-RAY DIFFRACTION9.274TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.080.50681570.44483008316599
3.08-3.240.38821580.329329833141100
3.24-3.450.41671450.36452758290391
3.45-3.710.42421110.32352126223770
3.71-4.090.3051280.27322424255280
4.09-4.680.26661580.208930043162100
4.68-5.890.2241580.21862997315599
5.89-37.650.24871570.18972973313098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3968-1.1567-1.48014.19172.11581.19840.07670.6402-0.4996-1.3180.64211.38611.0216-0.092-0.53211.011-0.2142-0.3931.21230.07421.729923.538937.4818-51.7814
24.85540.0609-0.31333.30822.2662.11291.63531.8151.0066-1.8858-1.0221.2802-2.2457-0.7493-0.61311.2607-0.08110.03341.59170.28391.97143.639147.9731-44.0995
3-0.3335-0.657-0.04011.4068-0.22881.32920.06820.2105-0.5551-0.5367-0.03320.55170.0874-0.3986-0.07680.6864-0.2762-0.09530.93240.0270.868431.521130.5886-48.1889
41.7341-2.68110.07124.44330.81412.9146-0.0832-0.0587-0.2109-0.3227-0.06870.33350.1283-0.32920.09410.4735-0.092-0.12580.59530.05550.749443.445334.2268-39.4412
51.6596-1.2805-1.44666.12683.30752.1233-0.0524-0.3184-0.4427-1.64450.0946-0.02730.7418-0.4553-0.09270.8671-0.0796-0.08890.7890.04180.895345.875526.805-47.8558
63.5595-0.5147-0.05594.9681-0.42491.9285-0.22680.6263-0.0258-0.67310.2003-0.24440.01610.02640.0280.6991-0.223-0.05850.7195-0.01330.571752.13631.9836-50.9055
72.3986-0.6941-0.43664.23385.1344.0424-0.3317-0.0789-1.19450.93540.5102-0.15121.24460.18360.07941.2854-0.11220.14690.79550.28511.883143.6182-11.0457-19.8715
81.9988-0.3869-0.20444.58630.16690.0155-0.34720.7244-0.8041-1.7507-0.46442.3159-0.0402-0.07450.53961.597-0.3710.02611.0413-0.16792.112336.5133-26.7803-30.2772
90.696-0.3576-0.52784.4589-0.32311.7792-0.1945-0.1869-0.20280.25490.2895-0.06920.1205-0.0269-0.10430.5225-0.0418-0.05690.58590.05280.736151.053223.6061-23.8911
100.9965-0.17951.07974.8426-0.24862.8488-0.0812-0.563-0.38870.43470.32880.06830.19590.0119-0.31990.6271-0.027-0.04980.58040.09080.680155.763321.2252-16.6028
112.31380.31920.05717.5352-0.1162.6390.0333-0.1644-0.20660.9032-0.0403-0.39730.02120.17050.09830.4122-0.0286-0.02910.5932-0.01120.658454.32528.4929-20.9971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 82 )A39 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 124 )A83 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 233 )A125 - 233
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 329 )A234 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 360 )A330 - 360
6X-RAY DIFFRACTION6chain 'A' and (resid 361 through 506 )A361 - 506
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 122 )B39 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 169 )B123 - 169
9X-RAY DIFFRACTION9chain 'B' and (resid 170 through 329 )B170 - 329
10X-RAY DIFFRACTION10chain 'B' and (resid 330 through 401 )B330 - 401
11X-RAY DIFFRACTION11chain 'B' and (resid 402 through 506 )B402 - 506

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