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- PDB-4gyi: Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate co... -

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Basic information

Entry
Database: PDB / ID: 4gyi
TitleCrystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium thermophilum
ComponentsRio2 kinase
KeywordsTRANSFERASE / protein kinase / ADP complex / phosphoaspartate / acyl-phosphate / ribosome biogenesis / ser/thr protein kinase / Ribosomal RNA processing / pre-40S maturation / pre-40S / Phosphorylation
Function / homology
Function and homology information


preribosome, small subunit precursor / maturation of SSU-rRNA / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity ...preribosome, small subunit precursor / maturation of SSU-rRNA / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / : / RIO domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / : / RIO domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFerreira-Cerca, S. / Sagar, V. / Schafer, T. / Diop, M. / Wesseling, A.M. / Lu, H. / Chai, E. / Hurt, E. / LaRonde-LeBlanc, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.
Authors: Ferreira-Cerca, S. / Sagar, V. / Schafer, T. / Diop, M. / Wesseling, A.M. / Lu, H. / Chai, E. / Hurt, E. / Laronde-Leblanc, N.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rio2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3475
Polymers44,7721
Non-polymers5764
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.624, 119.624, 71.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Rio2 kinase


Mass: 44771.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033330, Rio2 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(TM) PLysS / References: UniProt: G0S5R3
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE AS PROVIDED, INCLUDING RESIDUES 1-23 IS THE CORRECT SEQUENCE OF THE PROTEIN. THE ...THE SEQUENCE AS PROVIDED, INCLUDING RESIDUES 1-23 IS THE CORRECT SEQUENCE OF THE PROTEIN. THE UNIPROT DATABASE HAVE BEEN NOTIFIED OF THE ERROR

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 14-16% Poly-ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2011
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 19451 / Num. obs: 19451 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 38.55 Å2 / Rsym value: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 2.61→2.77 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.0796 / Num. unique all: 1940 / Rsym value: 0.144 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQP

1tqp


Resolution: 2.2→34.532 Å / SU ML: 0.31 / Isotropic thermal model: anisotropic TLS / σ(F): 0.13 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1880 10.14 %RANDOM
Rwork0.1682 ---
all0.1885 19451 --
obs0.174 18535 95.27 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.954 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.8381 Å20 Å2-0 Å2
2--1.8381 Å20 Å2
3----3.6761 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 36 104 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092791
X-RAY DIFFRACTIONf_angle_d1.2143773
X-RAY DIFFRACTIONf_dihedral_angle_d15.7941064
X-RAY DIFFRACTIONf_chiral_restr0.078414
X-RAY DIFFRACTIONf_plane_restr0.005476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1998-2.25930.23761290.20561150X-RAY DIFFRACTION85
2.2593-2.32580.29341360.19671190X-RAY DIFFRACTION89
2.3258-2.40080.31411390.20951229X-RAY DIFFRACTION91
2.4008-2.48660.29361400.19581238X-RAY DIFFRACTION92
2.4866-2.58620.27931360.21231247X-RAY DIFFRACTION94
2.5862-2.70380.25561590.19241289X-RAY DIFFRACTION96
2.7038-2.84630.25571550.19771292X-RAY DIFFRACTION97
2.8463-3.02450.26151530.18581311X-RAY DIFFRACTION98
3.0245-3.25790.25651400.17271326X-RAY DIFFRACTION98
3.2579-3.58540.24191520.1741343X-RAY DIFFRACTION99
3.5854-4.10350.19961470.16531344X-RAY DIFFRACTION100
4.1035-5.16720.19431420.12771362X-RAY DIFFRACTION100
5.1672-34.53670.17991520.15621334X-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)
15.6126-1.9815-1.22594.32290.7073.02590.09170.28850.0902-0.06370.0143-0.59620.17950.4959-0.05840.31660.27590.02080.5805-0.07740.357942.551915.2265-32.8661
22.94520.42820.780.22620.17072.76130.04180.1853-0.0141-0.1478-0.03970.01370.23360.21380.00690.27290.09840.0020.1112-0.02280.262922.347420.1477-27.6501
33.3677-0.0761-0.36781.70050.27573.33990.116-0.369-0.00470.12890.03290.30440.0965-0.5625-0.09250.2109-0.04420.01970.22490.01730.27863.609821.7678-17.4982
48.3609-5.73831.95434.7206-1.53318.7872-0.4425-0.66350.42361.73190.52560.2789-0.2513-0.7039-0.02420.38030.05250.05150.3754-0.05480.34823.142320.1775-11.1522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:76 )A2 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:176 )A77 - 176
3X-RAY DIFFRACTION3( CHAIN A AND RESID 177:321 )A177 - 321
4X-RAY DIFFRACTION4( CHAIN A AND RESID 322:341 )A322 - 341

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