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- PDB-6fdo: Rio2 structure -

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Basic information

Entry
Database: PDB / ID: 6fdo
TitleRio2 structure
ComponentsSerine/threonine-protein kinase RIO2
KeywordsHYDROLASE / kinase
Function / homology
Function and homology information


positive regulation of ribosomal small subunit export from nucleus / positive regulation of rRNA processing / regulation of mitotic metaphase/anaphase transition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity ...positive regulation of ribosomal small subunit export from nucleus / positive regulation of rRNA processing / regulation of mitotic metaphase/anaphase transition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RIO kinase, conserved site / Serine/threonine-protein kinase Rio2 / RIO1/ZK632.3/MJ0444 family signature. / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase RIO2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsFribourg, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR RIBOPRE40S France
CitationJournal: Rna Biol. / Year: 2019
Title: In vitro dimerization of human RIO2 kinase.
Authors: Maurice, F. / Perebaskine, N. / Thore, S. / Fribourg, S.
History
DepositionDec 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Sep 11, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase RIO2
B: Serine/threonine-protein kinase RIO2


Theoretical massNumber of molelcules
Total (without water)81,4642
Polymers81,4642
Non-polymers00
Water1,09961
1
A: Serine/threonine-protein kinase RIO2


Theoretical massNumber of molelcules
Total (without water)40,7321
Polymers40,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase RIO2


Theoretical massNumber of molelcules
Total (without water)40,7321
Polymers40,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.555, 67.555, 312.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine/threonine-protein kinase RIO2 / RIO kinase 2


Mass: 40732.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BVS4, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Morpheus D2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→42.69 Å / Num. obs: 279056 / % possible obs: 99.98 % / Redundancy: 11.3 % / Biso Wilson estimate: 83.28 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.0578 / Net I/σ(I): 8.73
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 31169 / CC1/2: 0.493 / Rpim(I) all: 0.7321 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→42.69 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.402 / SU Rfree Blow DPI: 0.271 / SU Rfree Cruickshank DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1193 4.85 %RANDOM
Rwork0.195 ---
obs0.198 24612 100 %-
Displacement parametersBiso mean: 81.33 Å2
Baniso -1Baniso -2Baniso -3
1-4.1775 Å20 Å20 Å2
2--4.1775 Å20 Å2
3----8.3549 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.6→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 0 61 4675
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014714HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.26357HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1675SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes798HARMONIC5
X-RAY DIFFRACTIONt_it4714HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion20.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5297SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3326 147 4.92 %
Rwork0.2294 2838 -
all0.2343 2985 -
obs--99.83 %
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)
11.722-0.05620.57222.2370.20942.65830.03250.24510.01680.1252-0.0413-0.2182-0.10630.60580.0087-0.41360.1184-0.071-0.2161-0.1043-0.43570.4745-8.782211.1506
23.0454-0.84020.15723.6990.31321.7514-0.09130.0837-0.55470.1679-0.12620.60030.1406-0.26710.2175-0.44640.1169-0.0169-0.3486-0.2238-0.251547.61-19.79518.4806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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