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- PDB-7kjt: KEOPS tRNA modifying sub-complex of archaeal Cgi121 and tRNA -

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Basic information

Entry
Database: PDB / ID: 7kjt
TitleKEOPS tRNA modifying sub-complex of archaeal Cgi121 and tRNA
Components
  • RNA (70-MER)
  • Regulatory protein Cgi121
KeywordsRNA BINDING PROTEIN/RNA / KEOPS / tRNA / Cgi121 / RNA modifying enzyme / N6-threonylcarbamoyl adenosine / RNA BINDING PROTEIN-RNA complex
Function / homologyCGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / : / RNA / RNA (> 10) / Regulatory protein Cgi121
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.34 Å
AuthorsCeccarelli, D.F. / Beenstock, J. / Mao, D.Y.L. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 143277 Canada
CitationJournal: Nat Commun / Year: 2020
Title: A substrate binding model for the KEOPS tRNA modifying complex.
Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / ...Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / Schriemer, D.C. / Bayfield, M.A. / Durocher, D. / Sicheri, F.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (70-MER)
H: Regulatory protein Cgi121


Theoretical massNumber of molelcules
Total (without water)41,5062
Polymers41,5062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, NMR HSQC and Fluorescence polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-0 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.284, 121.284, 91.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain RNA (70-MER)


Mass: 24413.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pUC19 / Details (production host): hepatitis delta virus ribozyme
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 6626255
#2: Protein Regulatory protein Cgi121 / Positive regulator of Bud32 kinase activity


Mass: 17092.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: cgi121, MJ0187 / Plasmid: pGEX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57646

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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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 200 mM lithium sulfate, 25% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 3.34→60.62 Å / Num. obs: 11643 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
3.34-3.439.91.428521100
14.94-60.628.60.025157198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.46 Å52.52 Å
Translation6.46 Å52.52 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ENH

3enh


Resolution: 3.34→36.58 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 593 5.11 %
Rwork0.2148 11018 -
obs0.2158 11611 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 406.53 Å2 / Biso mean: 143.5148 Å2 / Biso min: 57.35 Å2
Refinement stepCycle: final / Resolution: 3.34→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 1486 0 0 2600
Num. residues----215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.34-3.680.34121360.309927372873
3.68-4.210.24381560.229226982854
4.21-5.30.2311380.230627472885
5.3-36.580.21611630.184328362999
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)
13.7742.14760.13093.78863.01445.4511-0.7620.71480.7956-0.8697-0.06910.6187-0.6785-1.4060.25760.639-0.0065-0.05150.38660.05560.3801-56.757345.6888-16.0026
29.3398-8.00237.75029.6472-6.82417.3583-0.0488-0.7117-2.19840.22170.73361.97071.1682-1.71142.57360.8036-0.20730.32760.886-0.17020.9433-66.684232.9717-9.6337
31.804-1.1169-0.5794.6563.34822.47550.38610.45150.2-1.13030.3465-1.0924-0.93340.23662.36861.26310.1801-0.50690.2822-0.12540.4527-64.73055.8751-7.9032
45.0658-2.7556-5.97277.16483.48237.0347-0.9562-1.21470.48890.13041.0645-1.35890.14080.9248-2.06951.70150.3001-0.0640.6812-0.17930.6721-70.8543-2.55271.4662
50.0866-0.8411-0.05317.18621.50184.7043-0.22620.34920.4122-0.9167-0.37620.3417-0.5232-1.00470.52721.15770.1539-0.0760.6442-0.10640.7403-69.7884-11.9656-3.7313
63.6054-4.1651-1.60768.13051.67832.8475-0.3577-0.1175-1.58741.60870.5381.3372.2217-1.634-1.01181.953-0.2156-0.32311.4877-0.14851.8899-86.7652-10.684412.335
70.7614-0.6795-2.124.86621.04795.77370.22080.47880.5248-1.1669-0.41680.4618-0.4469-0.39190.18811.63790.1965-0.27220.97460.13890.9072-67.9857-0.6239-16.2359
85.42390.00141.08328.4937-0.44963.9478-0.5635-1.9384-0.3774-2.3031-0.9988-1.06232.48390.63990.48031.44490.29580.09730.98240.00750.9398-46.676225.133-11.5215
94.867-4.55370.80895.0473-3.50859.6633-0.1767-0.41911.26060.57711.107-0.5182-1.6904-0.59050.19350.9719-0.3075-0.19350.75150.03880.7552-49.930848.7315-9.5872
106.7576-0.30535.52256.7793-1.05955.67860.01711.7011-0.0655-0.2133-0.2858-1.71190.37650.9197-0.87720.58980.0615-0.17920.64490.1380.6248-47.483242.1602-13.2524
111.8983-0.0850.81058.9906-6.29754.9739-0.536-0.50530.0555-0.47440.99020.72280.0998-2.50660.55050.83750.01690.18321.11920.00150.3524-59.5539.2808-3.7979
129.0745-5.9975-1.24785.79171.45790.8399-0.3024-1.6679-2.57350.81410.12321.20660.7626-0.9627-0.73331.18330.0624-0.11020.9240.23970.8161-52.126428.2652-2.5231
138.79187.8085-7.69968.8534-5.29521.99910.2381-1.029-0.80231.5544-0.5025-1.98470.59061.6733-0.89430.80930.1496-0.05120.5185-0.11250.7679-52.547934.7899-7.1885
146.77413.789-3.83036.7005-7.28148.9639-0.99651.6144-1.604-1.21820.0393-1.90533.6146-0.69860.44261.2209-0.04370.10650.9368-0.36060.9054-53.703230.073-16.0543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 80 through 133 )H80 - 133
2X-RAY DIFFRACTION2chain 'H' and (resid 134 through 147 )H134 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 10 )A1 - 10
4X-RAY DIFFRACTION4chain 'A' and (resid 11 through 15 )A11 - 15
5X-RAY DIFFRACTION5chain 'A' and (resid 16 through 25 )A16 - 25
6X-RAY DIFFRACTION6chain 'A' and (resid 26 through 46 )A26 - 46
7X-RAY DIFFRACTION7chain 'A' and (resid 47 through 71 )A47 - 71
8X-RAY DIFFRACTION8chain 'A' and (resid 72 through 76 )A72 - 76
9X-RAY DIFFRACTION9chain 'H' and (resid 3 through 17 )H3 - 17
10X-RAY DIFFRACTION10chain 'H' and (resid 18 through 37 )H18 - 37
11X-RAY DIFFRACTION11chain 'H' and (resid 38 through 50 )H38 - 50
12X-RAY DIFFRACTION12chain 'H' and (resid 51 through 57 )H51 - 57
13X-RAY DIFFRACTION13chain 'H' and (resid 58 through 67 )H58 - 67
14X-RAY DIFFRACTION14chain 'H' and (resid 68 through 79 )H68 - 79

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