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- PDB-8rbj: Structure of fungal tRNA ligase in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 8rbj
TitleStructure of fungal tRNA ligase in complex with RNA
Components
  • RNA
  • tRNA ligase
KeywordsLIGASE / tRNA ligase / RNA duplex / RNA processing / tRNA splicing
Function / homology
Function and homology information


GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / RNA ligase (ATP) / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / phosphoric diester hydrolase activity / ATP binding / metal ion binding / nucleus
Similarity search - Function
tRNA ligase Trl1, fungi / tRNA ligase, phosphodiesterase / tRNA ligase, kinase domain, fungi / Fungal tRNA ligase phosphodiesterase domain / tRNA ligase kinase domain / T4 RNA ligase 1, N-terminal / RNA ligase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / RNA / tRNA ligase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKopp, J. / Koehler, S. / Peschek, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)442512666 Germany
German Research Foundation (DFG)439669440 Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles.
Authors: Kohler, S. / Kopp, J. / Maiti, S. / Bujnicki, J.M. / Peschek, J.
History
DepositionDec 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA ligase
C: RNA
B: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6644
Polymers53,3173
Non-polymers3471
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-4 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)51.560, 75.360, 124.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein tRNA ligase


Mass: 48873.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0034810 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S6G2
#2: RNA chain RNA


Mass: 2221.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: protein concentration: 5.8 mg/ml protein:RNA ratio = 1:1.7 precipitant solution: 20 % PEG3350, 0.2 M potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 12, 2021
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.37→47.64 Å / Num. obs: 20384 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 45.35 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.355 / Rpim(I) all: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 2.37→2.46 Å / Rmerge(I) obs: 3.123 / Mean I/σ(I) obs: 1 / Num. unique obs: 2019 / CC1/2: 0.392 / Rpim(I) all: 0.856

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Processing

Software
NameVersionClassification
XDS20200131data reduction
Aimless0.7.12data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→47.64 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 1003 4.92 %
Rwork0.1782 19370 -
obs0.1803 20373 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.29 Å2
Refinement stepCycle: LAST / Resolution: 2.37→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 301 23 113 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673569
X-RAY DIFFRACTIONf_angle_d0.93894890
X-RAY DIFFRACTIONf_chiral_restr0.0511536
X-RAY DIFFRACTIONf_plane_restr0.0084575
X-RAY DIFFRACTIONf_dihedral_angle_d14.31261370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.50.33631390.28572718X-RAY DIFFRACTION99.9
2.5-2.650.26811160.24182736X-RAY DIFFRACTION100
2.65-2.860.28491570.23352722X-RAY DIFFRACTION99.97
2.86-3.140.23361240.20222751X-RAY DIFFRACTION99.97
3.14-3.60.2241620.17332735X-RAY DIFFRACTION100
3.6-4.530.18151470.14992790X-RAY DIFFRACTION100
4.53-47.640.19541580.15052918X-RAY DIFFRACTION99.81
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)
13.94500007189-0.8750830615871.600042425074.140467434350.2496223821543.297179228-0.451042754387-0.6795554162720.6892278044060.5471652963380.27839754010.54362712012-1.03230293722-0.8603385634040.1667404649660.5932080273770.1770720076660.1134145474960.672971726717-0.07041212150320.606780977242-20.6961.69227.718
24.648582722630.545632053715-0.734312786014.299310114090.1575916385185.541408261890.2264228559550.0817930363052-1.08363854947-0.1226966182720.0476947440861-0.5480556436061.1134938539-0.0414517483974-0.2670884535760.5449715332220.0705997361441-0.1607300212080.269044301983-0.03039871375780.595918475209-2.498-24.46720.522
33.875390549631.392943109751.333099467472.82432231330.4315843628433.878352302220.4616867005140.0872306056729-1.11005597179-0.5528706632690.04370590177390.2514211795671.1456316627-0.342430723023-0.5008005224710.521300778886-0.147147770092-0.1718439549690.369968704278-0.003333276311390.583111570007-12.258-21.67914.53
44.22475887231-0.147569992120.7314664060543.37571508857-0.8757018850414.6547891733-0.02749362035310.0757409944383-0.171962249194-0.1056629842210.2420498877570.1141324283390.301377468127-0.704354918663-0.1698724958750.256363418144-0.0336954903809-0.01383827398520.288192271308-0.008926316292170.230527194515-11.765-11.25518.169
52.239523314980.4706526731370.7644963362674.95988100385-0.4395404600482.53028834674-0.148001822497-0.09930620342180.2523338829660.446847205246-0.0655738763461-0.649581617035-0.7410824622930.3171570805150.2087130718020.4103329901430.0119875318704-0.0858154564960.290358250347-0.04644240850010.4179658737561.1950.10124.851
63.73365553718-0.6914176588860.8404055093662.15837827503-0.006494900468425.42467856217-0.1558622468050.03612510201690.4152513187050.1317285862610.07746384003440.133886507674-0.81026699292-0.5379190422290.03541883046130.330988705480.081667676921-0.01923463409310.271575155841-0.01933950986950.289584980171-11.951-0.12219.813
75.171212201382.50134917069-0.6672168309253.7707328319-0.1323294706713.801947659720.1560359815060.4237357792510.764390474058-0.162399759189-0.03629571662850.750795283372-1.27213785085-1.34400103210.006228990189980.700826588060.360727674767-0.1244601677631.030486627490.1218082457920.667644390759-28.5314.2369.575
85.183742063260.294744851519-1.904934503463.994774655210.6140307035324.51862764906-0.0851056145388-0.0992792164186-0.614022994363-0.01098779826070.1723564171910.8459636916170.27913178828-1.663043413540.0115982388570.295289182607-0.012236514462-0.03600670295130.8506827353720.09684643630080.528175367674-26.347-9.27617.18
96.68468226671-1.27651566968-3.177684638931.684312428480.7673461212963.95363055007-0.1126340017630.371643187572-0.711717304157-0.220178580358-0.02625474897160.04157155303060.09487353397630.195246522935-0.05331204762650.7814382877750.116596076079-0.002734663337480.8800461519650.08308424443120.466043180738-13.704-0.546-10.897
103.193209554360.330715961312-0.9843434385832.844681978990.1566611580834.142789278450.2632862984480.7552535770220.364869147083-0.709081165541-0.352453306837-0.365875202179-0.4507990332560.8961971001640.1097709277121.168243450120.009501225232870.02535987150781.127105673030.2957922175080.561906920609-7.0277.784-12.46
117.73930518819-1.324666300960.7774254463432.55664954081-0.6660687129082.95781812904-0.722902680559-0.06892824842840.6233550666590.2114081600580.608871186410.221319368391-1.11002401354-0.4837821890110.2252197086341.053516958560.196448068242-0.02876614444050.766298490450.2583279962910.707363067867-18.16111.544-6.564
121.786867939035.001380172814.752140146514.275254020049.105189419338.90033273767-0.52502973482-0.1374572178820.334414431783-0.5897467561850.379159742360.0851086566174-0.8886578679470.4498141551780.04259176787080.5937252685120.00896403296848-0.1959053529060.618692253117-0.09040368504840.523423236708-23.089-18.833-0.101
138.563534921253.212276022730.565779418724.7110864513-1.01062971173.24178650328-0.94992984471-1.01195570723-0.1635530171862.488338643550.576735872269-0.152655540144-0.515461167776-0.434575985610.09293174873010.9338589867420.0616638237525-0.2676748935851.1760386508-0.2766251985040.515235782827-29.503-26.0592.674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:37 )A12 - 37
2X-RAY DIFFRACTION2( CHAIN A AND RESID 38:77 )A38 - 77
3X-RAY DIFFRACTION3( CHAIN A AND RESID 78:100 )A78 - 100
4X-RAY DIFFRACTION4( CHAIN A AND RESID 101:181 )A101 - 181
5X-RAY DIFFRACTION5( CHAIN A AND RESID 182:210 )A182 - 210
6X-RAY DIFFRACTION6( CHAIN A AND RESID 211:277 )A211 - 277
7X-RAY DIFFRACTION7( CHAIN A AND RESID 278:300 )A278 - 300
8X-RAY DIFFRACTION8( CHAIN A AND RESID 301:329 )A301 - 329
9X-RAY DIFFRACTION9( CHAIN A AND RESID 330:354 )A330 - 354
10X-RAY DIFFRACTION10( CHAIN A AND RESID 355:384 )A355 - 384
11X-RAY DIFFRACTION11( CHAIN A AND RESID 385:407 )A385 - 407
12X-RAY DIFFRACTION12( CHAIN B AND RESID 2:8 )B2 - 8
13X-RAY DIFFRACTION13( CHAIN C AND RESID 2:8 )C2 - 8

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