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- PDB-7kju: Cgi121-tRNA complex -

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Basic information

Entry
Database: PDB / ID: 7kju
TitleCgi121-tRNA complex
ComponentsRNA (75-MER)
KeywordsRNA / KEOPS / tRNA / Cgi121 / RNA modifying enzyme / N6-threonylcarbamoyl adenosine
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsCeccarelli, D.F. / Beenstock, J. / Wan, L.C.K. / 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 / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / 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_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _ndb_struct_conf_na.feature / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _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_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _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.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.classification / _software.name / _software.version / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: Frameshift 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 (75-MER)


Theoretical massNumber of molelcules
Total (without water)24,7591
Polymers24,7591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.493, 168.527, 68.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: RNA chain RNA (75-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: 2045106419
Has ligand of interestN
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: 5.98 Å3/Da / Density % sol: 79.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 0.2 M zinc acetate, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97964 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 3.1→49.14 Å / Num. obs: 10895 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.025 / Rrim(I) all: 0.085 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.11-3.198.90.93170167920.9560.330.9892.1100
13.91-49.149.50.03612111270.9990.0120.03836.887.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.11 Å49.03 Å
Translation3.11 Å49.03 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 3L0U

3l0u


Resolution: 3.1→49.03 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 603 5.6 %
Rwork0.2271 --
obs0.2283 10777 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1640 0 0 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021830
X-RAY DIFFRACTIONf_angle_d0.4522852
X-RAY DIFFRACTIONf_dihedral_angle_d22.6761167
X-RAY DIFFRACTIONf_chiral_restr0.022385
X-RAY DIFFRACTIONf_plane_restr0.00277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.28121460.2842412X-RAY DIFFRACTION95
3.41-3.910.28711510.24662512X-RAY DIFFRACTION98
3.91-4.920.26111310.2522596X-RAY DIFFRACTION100
4.93-49.030.23021750.20582654X-RAY DIFFRACTION99
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)
13.24680.18310.16181.8606-2.12762.52250.1585-0.71880.25140.51320.19890.34850.1614-0.6802-0.44580.54070.14510.15050.9307-0.10210.727531.6338.88699.2585
29.8236-3.1022-0.29849.4668-0.23762.72921.2281.40150.6116-1.8271-0.97380.4145-1.76640.5743-0.40822.45980.33030.01541.65860.07971.830935.285134.0216-7.7795
36.73640.33-2.76233.4324-0.36473.40780.095-1.56950.51330.75420.05410.6290.1514-0.3358-0.12640.90190.12830.01161.32830.05560.693931.2190.297920.7658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 76 )

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