[English] 日本語
Yorodumi
- PDB-6fdm: Human Rio2 kinase structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fdm
TitleHuman Rio2 kinase structure
ComponentsSerine/threonine-protein kinase RIO2
KeywordsTRANSFERASE / kinase / RIBOSOME
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 / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase RIO2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsFribourg, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-05 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 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Sep 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 1.4Oct 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 1.5May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase RIO2
B: Serine/threonine-protein kinase RIO2
C: Serine/threonine-protein kinase RIO2
D: Serine/threonine-protein kinase RIO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4538
Polymers145,3954
Non-polymers1,0584
Water10,737596
1
A: Serine/threonine-protein kinase RIO2
B: Serine/threonine-protein kinase RIO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2274
Polymers72,6972
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area26600 Å2
MethodPISA
2
C: Serine/threonine-protein kinase RIO2
D: Serine/threonine-protein kinase RIO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2274
Polymers72,6972
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-22 kcal/mol
Surface area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.920, 98.327, 117.069
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 36348.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BVS4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen D2

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 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: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→66.64 Å / Num. obs: 331294 / % possible obs: 98.49 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.69 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0216 / Net I/σ(I): 20.59
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.32 / Num. unique obs: 31840 / CC1/2: 0.879 / Rpim(I) all: 0.3359 / % possible all: 96.68

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→66.64 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.9284 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 4366 5.03 %RANDOM
Rwork0.2016 ---
obs0.2034 86873 98.59 %-
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.4661 Å20 Å2-3.5416 Å2
2---9.9792 Å20 Å2
3---4.5131 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: 1 / Resolution: 2.1→66.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9194 0 64 596 9854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019458HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0612761HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3367SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes235HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1378HARMONIC5
X-RAY DIFFRACTIONt_it9458HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion18.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1186SEMIHARMONIC5
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_contact11243SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2577 313 5.03 %
Rwork0.2222 5914 -
all0.2239 6227 -
obs--98.59 %
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)
12.5949-0.1622-0.3621.07090.18582.13440.0174-0.38150.01870.12680.0756-0.05310.0851-0.1538-0.093-0.25240.07830.0046-0.073-0.0224-0.269352.44492.1052175.4511
21.85850.63670.31111.88270.78742.4140.07230.0783-0.0799-0.04530.0619-0.19970.09-0.1212-0.1342-0.20610.0660.0454-0.19020.0401-0.263253.0973-3.854151.3545
32.3261-0.2123-0.57031.2768-0.24731.8570.10930.05510.0346-0.15860.05040.07530.02990.1412-0.1596-0.264-0.05630.0114-0.1730.0221-0.277989.180744.6937116.0901
41.7771-0.84540.12362.1556-0.22051.20290.0134-0.2924-0.01630.17690.17090.11690.05430.0867-0.1842-0.1982-0.00540.0541-0.1252-0.011-0.279888.319639.2947140.2028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more