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- PDB-8btt: Structure of human RTCB -

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Basic information

Entry
Database: PDB / ID: 8btt
TitleStructure of human RTCB
ComponentsRNA-splicing ligase RtcB homolog
KeywordsLIGASE / human / tRNA splicing
Function / homology
Function and homology information


: / tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / placenta development / nuclear envelope / in utero embryonic development ...: / tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / placenta development / nuclear envelope / in utero embryonic development / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / GTP binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA-splicing ligase RtcB homologue, eukaryotic / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB
Similarity search - Domain/homology
: / RNA-splicing ligase RtcB homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKopp, J. / Gerber, J.L. / Peschek, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)442512666 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
Authors: Gerber, J.L. / Morales Guzman, S.I. / Worf, L. / Hubbe, P. / Kopp, J. / Peschek, J.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _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: RNA-splicing ligase RtcB homolog
B: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8834
Polymers116,7732
Non-polymers1102
Water66737
1
A: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4412
Polymers58,3871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4412
Polymers58,3871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.640, 215.640, 46.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase


Mass: 58386.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTCB, C22orf28, HSPC117 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein: 125 uM in 25 mM Tris pH 7.5, 200 mM NaCl, 10 % glycerol, 1mM TCEP, 2 mM manganese chloride reservoir: 0.1 M magnesium chloride, 0.1 M HEPES pH 7.0, 15 % PEG 4000 drop: 800 nl protein + 600 nl reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→48.22 Å / Num. obs: 33777 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4030 / CC1/2: 0.348 / Rpim(I) all: 0.875

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless1.12.10data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model for Q9Y3I0

Resolution: 2.6→48.22 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 1722 5.1 %
Rwork0.1992 32049 -
obs0.202 33771 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7490 0 2 37 7529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00267628
X-RAY DIFFRACTIONf_angle_d0.517110296
X-RAY DIFFRACTIONf_chiral_restr0.0441134
X-RAY DIFFRACTIONf_plane_restr0.00391352
X-RAY DIFFRACTIONf_dihedral_angle_d13.42152821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.35471550.2942580X-RAY DIFFRACTION100
2.68-2.760.32981480.27282676X-RAY DIFFRACTION100
2.76-2.860.3381350.28872620X-RAY DIFFRACTION99.96
2.86-2.980.32881460.25412643X-RAY DIFFRACTION100
2.98-3.110.31151530.25272660X-RAY DIFFRACTION100
3.11-3.280.26371490.22172625X-RAY DIFFRACTION100
3.28-3.480.29221320.21342674X-RAY DIFFRACTION99.96
3.48-3.750.27821520.18762657X-RAY DIFFRACTION100
3.75-4.130.2271240.17482685X-RAY DIFFRACTION100
4.13-4.720.20991490.16052689X-RAY DIFFRACTION99.93
4.72-5.950.23921450.19022720X-RAY DIFFRACTION99.97
5.95-48.220.22311340.1862820X-RAY DIFFRACTION99.9
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)
11.66569708141-0.6835136436470.2540321287660.779544780769-0.7961831628191.00419329277-0.0537444705408-0.1321781863180.5556716890490.2488759231680.0484344177441-0.509393640479-0.3653531884550.4284843855273.12280579507E-60.837789993991-0.1272940591880.09413516593030.7120814559590.0004857242039371.21432102826148.64978984281.727430996-8.40063939937
22.95296671336-0.211306656883-0.3108442733051.86100550672-0.2617558619020.9875393576740.0290565357925-0.2802078835640.2734304894220.1108275478490.0090124750016-0.220122418255-0.220818763285-0.05286686317280.0004449820206710.6256120986710.0325974140494-0.03978457651330.585444999741-0.1672835911130.510904379682128.80735525967.48217688871.92783519929
31.888428509930.153147378868-0.8741437078341.557961731410.01221279628960.3945474476720.0208951526147-0.0190112227443-0.3770054167730.1560833074350.06988651710880.02980787254630.0576649034384-0.02152843089623.86495612736E-50.5949015696730.0302450507589-0.05424517979150.593742114711-0.08483927782670.413696304328124.7678835955.78352644964.87563467502
42.865765356330.214131749404-1.415206211612.73826228688-0.4167411780820.701672908743-0.120101741452-0.006540425015920.2830251617840.2573119521650.120717913430.3588170499-0.438184130197-0.1017334640290.0001860479981540.5759048250520.1002435460350.001852285030760.642943093095-0.06474268675080.586467035797115.26577798772.2140063742-2.32866399061
50.4759619505150.6740429315430.2014203536991.38281510708-0.5682124097951.546962488430.175151336882-0.9141419511070.2998694595160.481263045554-0.150337992324-0.724162464543-0.115740384960.359085570512-1.4025268563E-50.6377273040040.0495580144686-0.1694427235040.744937290783-0.1572182713870.946882781519146.77937480762.45879886537.7267742934
62.78651768321-0.354114820121-0.2560817216091.97139108779-0.2572315794341.055982332270.05009296053820.06984550400910.477182001854-0.1360618242480.0773330778783-0.177099047481-0.210198500102-0.115859648097-0.002021554274810.434613367018-0.003467631701120.001938076347180.397545069548-0.07317300438110.36199086413123.79872067569.3521265466-4.23501229243
72.359317469610.268789157522-0.5222280959281.39849436787-0.8797478095830.881551393174-0.2148569470180.22668196011-0.2608714388090.06819759054930.03267839534370.1977143288390.308695011221-0.4451804234535.33339212862E-50.602298991343-0.05079891456340.1160967541140.6024667484930.03503180472060.68507127214363.658833951424.99899877658.97771257069
81.638366077770.2228642296870.0996730536761.016000459810.4545973760910.809256463038-0.11119936971-0.414054312057-0.7012127393390.5281766344770.171816818616-0.02001402416760.4263484007230.1047225075290.0003655384336860.696608833454-0.0006349136992650.06628396141120.6189093563660.08025754423580.74197042507772.302993604122.94685730699.80466309226
91.717453530161.19685642792-0.9415466459172.272458830270.1200544306890.6467039178280.14945216138-0.04466916624620.09126879188260.00365512212179-0.003103805971820.2353434603540.01071284948350.02831008204861.42322959316E-50.5786435451830.04029589080940.07475174606080.6309440692290.06140121335870.49780240820679.576438994739.00688002536.59864819772
100.7299273261070.539795216061-0.1982007304240.359582686717-0.09848706245660.0240425940015-0.0749585591651-1.02086940271-0.3642367513950.8593803283080.399531935709-1.66194258980.1255904348740.8925664681-2.01887354112E-50.854157971711-0.0135212005925-0.2576935506050.8353791809890.1556817664731.18990121419109.45779723237.388532430912.7443520898
111.751020647740.209828237728-0.4483800332771.51273016297-0.4743413485540.2496311737240.07744944129010.4509714534320.9177097470410.3117045613490.04769560113350.0986852227676-0.103731756301-0.04622369818035.32107471101E-50.654460311329-0.02451329637810.05633086932340.6376878581690.03986011931580.71790850224693.713571536155.05281195858.01331073179
124.087884879840.403916928008-0.5528995754562.951356222890.006825498437210.06890770200720.0554102315687-0.196135394919-0.5654730364770.1875734184750.123347237294-0.7237683293450.2324160085210.2229465021940.0002469420367550.643956162752-0.0185394450871-0.004329869973660.6270021182140.0876560577310.61276287421198.560272647237.29376687615.95935013432
130.5101922292230.3886122138390.3225058570580.2875878440670.08460199169541.019396617130.272723265086-0.791472502250.4517108284550.710686489422-0.1006891334410.419442101276-0.3287181461-0.1935008302890.000181338325670.866954886018-0.07260979161360.2505678038250.7262737663640.03209969260340.88495023387371.463401899245.789890706619.2529209522
141.052835530120.769189701545-0.2282998398932.300259499940.3315710644140.58282892906-0.01962411970670.04856176885940.02467644009250.06430783736730.0461784692882-0.100705019184-0.02593369803240.1465676929148.39523084308E-60.576713628444-0.03644095584050.05215355234410.6226329655540.03953531426620.48793002980294.752487856445.86316899856.08339150762
152.177218266060.85667301877-1.173637925152.018587170050.3853324873271.6316098681-0.07560957197010.733846766799-0.195707796483-0.3921022179320.140388809170.1494362254410.0940799020075-0.0827879240414-0.0001733658820490.624372784396-0.04250818940550.02847267534120.7825380159640.04813780568720.52302616943584.112463831438.6594208352-4.19831141727
161.711766102411.83728386101-0.1760989827862.142629216250.162856988690.603196273127-0.255336543805-0.552517556678-0.7091204694590.3531536933460.0820133406861-0.6426489636910.0158306214398-0.191644009586-0.003869265874860.6609141408370.03187270874590.0478303596610.5717313007370.06353765981090.68000357748494.425702143325.85815927197.48417075966
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -9 through 55 )AA-9 - 551 - 65
22chain 'A' and (resid 56 through 182 )AA56 - 18266 - 187
33chain 'A' and (resid 183 through 215 )AA183 - 215188 - 220
44chain 'A' and (resid 216 through 262 )AA216 - 262221 - 267
55chain 'A' and (resid 263 through 300 )AA263 - 300268 - 305
66chain 'A' and (resid 301 through 505 )AA301 - 505306 - 490
77chain 'B' and (resid -7 through 32 )BC-7 - 321 - 40
88chain 'B' and (resid 33 through 74 )BC33 - 7441 - 78
99chain 'B' and (resid 75 through 132 )BC75 - 13279 - 136
1010chain 'B' and (resid 133 through 164 )BC133 - 164137 - 162
1111chain 'B' and (resid 165 through 208 )BC165 - 208163 - 206
1212chain 'B' and (resid 209 through 262 )BC209 - 262207 - 260
1313chain 'B' and (resid 263 through 300 )BC263 - 300261 - 298
1414chain 'B' and (resid 301 through 363 )BC301 - 363299 - 361
1515chain 'B' and (resid 364 through 422 )BC364 - 422362 - 420
1616chain 'B' and (resid 423 through 505 )BC423 - 505421 - 484

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