[English] 日本語
Yorodumi
- PDB-3raw: Crystal Structure of human CDC-like kinase 3 isoform in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3raw
TitleCrystal Structure of human CDC-like kinase 3 isoform in complex with leucettine L41
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / KINASE / TYROSINE-PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3RA / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFilippakopoulos, P. / Fedorov, O. / King, O. / Debdab, M. / Carreaux, F. / Renault, S. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Fedorov, O. / King, O. / Debdab, M. / Carreaux, F. / Renault, S. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Meijer, L. / Bazureau, J.P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of human CDC-like kinase 3 isoform with a benzo-dioxol ligand
Authors: Filippakopoulos, P. / Fedorov, O. / King, O. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1954
Polymers89,5802
Non-polymers6152
Water4,432246
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0972
Polymers44,7901
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0972
Polymers44,7901
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 122.420, 69.280
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLUGLUAA136 - 23733 - 134
211VALVALGLUGLUBB136 - 23733 - 134
112LEULEUPHEPHEAA239 - 296136 - 193
212LEULEUPHEPHEBB239 - 296136 - 193
122GLUGLUSERSERAA297 - 310194 - 207
222GLUGLUSERSERBB297 - 310194 - 207
132VALVALGLYGLYAA311 - 410208 - 307
232VALVALGLYGLYBB311 - 410208 - 307
113ASPASPARGARGAA415 - 480312 - 377
213ASPASPARGARGBB415 - 480312 - 377

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 44790.062 Da / Num. of mol.: 2 / Fragment: Residues 275-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P49761, dual-specificity kinase
#2: Chemical ChemComp-3RA / 5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one


Mass: 307.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M NaNO3 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 5.4 / Number: 233131 / Rsym value: 0.091 / D res high: 2.09 Å / D res low: 36.263 Å / Num. obs: 59553 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.6136.2698.310.040.043.8
4.676.6199.310.0620.0623.9
3.824.6799.110.0630.0633.9
3.33.8299.110.0660.0663.9
2.963.398.810.0890.0893.9
2.72.9698.410.1270.1273.9
2.52.797.910.1910.1913.9
2.342.597.810.2990.2993.9
2.22.3497.910.4680.4683.9
2.092.297.110.7550.7553.9
ReflectionResolution: 2.09→36.263 Å / Num. all: 60645 / Num. obs: 59553 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.09-2.23.90.75513383886020.75597.1
2.2-2.343.90.4681.63191181230.46897.9
2.34-2.53.90.2992.53038677190.29997.8
2.5-2.73.90.1913.92806671400.19197.9
2.7-2.963.90.1275.52605366380.12798.4
2.96-3.33.90.0897.42359560230.08998.8
3.3-3.823.90.0668.92083553380.06699.1
3.82-4.673.90.0638.91753345150.06399.1
4.67-6.613.90.0627.91357435160.06299.3
6.61-36.2633.80.0413.5734019390.0498.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.26 Å
Translation2.5 Å36.26 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2EXE, 2EU9, 1Z57

2exe

2eu9

1z57


Resolution: 2.09→36.263 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1875 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU B: 8.663 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1611 / SU Rfree: 0.1498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1988 3.3 %RANDOM
Rwork0.1809 ---
all0.1822 60691 --
obs0.1822 59520 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.05 Å2 / Biso mean: 45.8424 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0.24 Å2
2--0.93 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 46 246 5895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215837
X-RAY DIFFRACTIONr_bond_other_d0.0010.023945
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9457908
X-RAY DIFFRACTIONr_angle_other_deg0.9233.0019517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71923.299288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86315962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7361539
X-RAY DIFFRACTIONr_chiral_restr0.0950.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
X-RAY DIFFRACTIONr_mcbond_it3.433491
X-RAY DIFFRACTIONr_mcbond_other1.45231410
X-RAY DIFFRACTIONr_mcangle_it4.90855610
X-RAY DIFFRACTIONr_scbond_it7.79182346
X-RAY DIFFRACTIONr_scangle_it9.579112298
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11267MEDIUM POSITIONAL0.220.5
11267MEDIUM THERMAL0.92
22361MEDIUM POSITIONAL0.150.5
22361MEDIUM THERMAL1.322
3919MEDIUM POSITIONAL0.340.5
3919MEDIUM THERMAL1.342
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 141 -
Rwork0.292 4212 -
all-4353 -
obs--97.4 %
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)
14.5626-0.7388-0.44757.0304-3.17283.8988-0.1248-0.1258-0.6616-0.3741-0.3192-0.82590.65040.38850.4440.32910.04210.07320.1677-0.04190.428887.681616.444214.9844
23.10440.1213-1.2361.65890.35563.9085-0.0264-0.18610.1256-0.0815-0.1322-0.06950.09510.28230.15870.01640.0251-0.01840.0926-0.02810.114186.3240.47720.3863
31.95780.46791.07280.91070.80214.248-0.08320.05940.5685-0.1947-0.01680.048-0.33250.19690.10.08270.0343-0.02960.0965-0.02690.284285.914750.662818.4345
46.45060.0640.10396.8418-2.0033.2274-0.0830.19750.79460.3785-0.1691-0.8719-0.42590.19450.25210.3350.0302-0.06260.11750.00310.404856.708472.231754.0112
53.5442-0.31630.44931.88120.40372.6986-0.04730.3279-0.24480.2129-0.09030.0889-0.0608-0.04790.13760.0299-0.01440.00670.0763-0.01570.068155.585148.612747.1668
62.605-0.6958-1.64372.06010.89684.0532-0.204-0.1812-0.68750.6119-0.04150.27410.53990.10920.24550.2373-0.05820.05620.11210.00160.320355.422238.17649.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 238
2X-RAY DIFFRACTION2A239 - 410
3X-RAY DIFFRACTION3A411 - 484
4X-RAY DIFFRACTION4B136 - 237
5X-RAY DIFFRACTION5B238 - 414
6X-RAY DIFFRACTION6B415 - 484

+
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