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- PDB-4otp: Crystal structure of the catalytic domain of the human RioK1 atyp... -

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Basic information

Entry
Database: PDB / ID: 4otp
TitleCrystal structure of the catalytic domain of the human RioK1 atypical protein kinase in complex with ADP/Mg2+
ComponentsSerine/threonine-protein kinase RIO1
KeywordsTRANSFERASE / atypical kinase domain / RIO domain / ribosome biogenesis / pre-40S / preribosome / phosphorylation
Function / homology
Function and homology information


methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / positive regulation of rRNA processing / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity ...methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / positive regulation of rRNA processing / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase Rio1 / : / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO1 family / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily ...Serine/threonine-protein kinase Rio1 / : / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO1 family / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase RIO1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLaRonde, N.A. / Kiburu, I.N.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes.
Authors: Ferreira-Cerca, S. / Kiburu, I. / Thomson, E. / LaRonde, N. / Hurt, E.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase RIO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2773
Polymers41,8251
Non-polymers4522
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.760, 78.760, 110.570
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: Protein Serine/threonine-protein kinase RIO1 / RioK1 / RIO kinase 1


Mass: 41825.223 Da / Num. of mol.: 1 / Fragment: RIO domain (UNP residues 143-494)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BRS2, non-specific serine/threonine protein kinase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 28% PEG400, 0.1 M HEPES, pH 7.5, 0.2 M calcium chloride, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→42.95 Å / Num. all: 11330 / Num. obs: 11336 / % possible obs: 99.95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 58.88 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.69
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 2 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1101 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→42.949 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 31.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2434 1083 10.15 %
Rwork0.2036 --
obs0.2077 10668 94.11 %
all-11336 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→42.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 28 7 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141956
X-RAY DIFFRACTIONf_angle_d1.32635
X-RAY DIFFRACTIONf_dihedral_angle_d20.095742
X-RAY DIFFRACTIONf_chiral_restr0.08291
X-RAY DIFFRACTIONf_plane_restr0.004334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82290.34481170.31611005X-RAY DIFFRACTION80
2.8229-2.97170.34391300.28531080X-RAY DIFFRACTION88
2.9717-3.15780.35751340.27661148X-RAY DIFFRACTION91
3.1578-3.40160.28491330.25481193X-RAY DIFFRACTION96
3.4016-3.74370.31551370.21071247X-RAY DIFFRACTION98
3.7437-4.2850.20451430.17131263X-RAY DIFFRACTION99
4.285-5.3970.20981420.16581281X-RAY DIFFRACTION100
5.397-42.95420.1981470.19171368X-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)
17.42574.12724.18326.11683.65413.6075-0.54451.5760.49250.22160.54450.37630.39672.1760.09122.04730.1458-0.10141.65230.1180.622630.027146.49996.6526
23.14530.20850.36442.1471-1.48573.3904-0.60210.22290.2108-0.24680.31750.0823-0.925-0.07630.27311.47630.2971-0.03161.1144-0.02980.531524.464844.594116.9876
32.1463-1.60331.08243.6327-0.03433.23040.26910.38570.4172-0.9025-0.3888-0.2427-0.20240.7586-1.72921.2610.5235-0.14230.9792-0.30090.476129.305832.474220.1483
41.64590.48010.18422.33910.38054.08220.42910.4136-0.4132-0.6338-0.19820.39390.32990.2003-0.12681.08640.4442-0.15320.8586-0.10520.604326.172733.68134.7157
54.6234-3.02960.06533.5915-1.69322.9263-0.2269-0.48160.61490.02790.1467-0.2736-0.90951.51590.49790.8530.2643-0.17751.1059-0.1380.548833.756134.493443.4232
66.1882-1.5176-0.40544.0842.4531.8071-0.0871-0.576-0.63110.2818-0.12970.30651.30550.341-0.0720.91920.3146-0.18120.535-0.02610.652228.56122.341548.3913
79.1627-3.4353-7.27264.10652.98556.47560.77320.11271.6286-0.5446-0.1225-0.4723-1.40570.1849-0.06620.88450.262-0.01291.23560.12440.566542.014731.374352.673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 175 )
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 277 )
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 352 )
5X-RAY DIFFRACTION5chain 'A' and (resid 353 through 371 )
6X-RAY DIFFRACTION6chain 'A' and (resid 372 through 410 )
7X-RAY DIFFRACTION7chain 'A' and (resid 411 through 430 )

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