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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
Revision 2.0Jun 25, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_radiation_wavelength / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_database_related / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands
Description: Model completeness
Details: frame-shift in tRNA nucleotide base pairing was identified and corrected
Provider: author / Type: Coordinate replacement

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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)41,8512
Polymers41,8512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR HSQC and Fluorescence polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2 kcal/mol
Surface area18500 Å2
Unit cell
Length a, b, c (Å)121.284, 121.284, 91.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain RNA (70-MER)


Mass: 24758.672 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
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: 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: 0.9792 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: 0.9792 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
PHENIX(1.21.1_5286: ???)refinement
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: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 593 5.11 %
Rwork0.2065 --
obs0.208 11611 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 1538 0 0 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022851
X-RAY DIFFRACTIONf_angle_d0.434201
X-RAY DIFFRACTIONf_dihedral_angle_d21.751528
X-RAY DIFFRACTIONf_chiral_restr0.029542
X-RAY DIFFRACTIONf_plane_restr0.003267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.680.36621360.30192737X-RAY DIFFRACTION100
3.68-4.210.27831560.25012698X-RAY DIFFRACTION100
4.21-5.30.24261380.22432747X-RAY DIFFRACTION100
5.3-36.580.20071630.16592836X-RAY DIFFRACTION100
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)
10.23672.6966-2.31121.4051-1.62051.4813-0.0314-0.37090.302-0.80530.0433-0.5334-1.15340.8837-0.06041.4844-0.0259-0.13110.7437-0.03760.9084-65.3405-0.7387-6.4875
22.7064-1.59962.61792.3211-0.4753.10330.57780.1606-0.4713-0.4999-0.39550.93520.5377-0.4224-0.00141.2102-0.1408-0.11570.8938-0.21641.1293-82.695-10.38987.1298
32.20532.1677-1.17822.6284-0.8546-1.7147-0.2457-0.26140.5201-1.16-0.12980.4881-0.1354-0.1474-0.00661.68540.0798-0.32890.950.06910.8726-63.32794.2149-15.8659
42.3751-0.0719-1.69670.5419-0.46531.4162-0.4463-0.24730.70390.26440.0032-0.56950.63510.8463-0.00011.0697-0.0501-0.03620.77630.01220.8501-45.685845.8041-10.4743
54.89530.26192.18862.5086-1.43481.8062-0.1288-0.0018-0.59320.1355-0.0454-0.17110.7098-0.1827-0.00010.97230.0870.0560.9144-0.00320.6449-54.913235.6115-9.0553
62.2596-0.48020.9622.0008-1.12820.8386-0.64991.306-0.0173-0.2740.4889-0.27161.16221.54010.05221.06090.04360.02760.99620.11920.7081-50.368444.9053-13.5294
77.3404-2.8662-3.18783.3449-1.74047.3046-0.85920.2312.5771-0.441-0.387-1.4516-3.88570.1426-2.8071.3543-0.0888-0.08990.7357-0.00661.1548-42.501151.3384-9.7567
84.78470.79690.1211.31722.12494.0737-0.17010.35120.85930.0133-0.84511.0196-0.9874-0.6575-0.56980.75390.01840.10520.7981-0.13590.6403-65.235740.1726-16.1418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 76 )
4X-RAY DIFFRACTION4chain 'H' and (resid 3 through 26 )
5X-RAY DIFFRACTION5chain 'H' and (resid 27 through 78 )
6X-RAY DIFFRACTION6chain 'H' and (resid 79 through 92 )
7X-RAY DIFFRACTION7chain 'H' and (resid 93 through 103 )
8X-RAY DIFFRACTION8chain 'H' and (resid 104 through 147 )

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