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- PDB-2wo6: Human Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase ... -

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Basic information

Entry
Database: PDB / ID: 2wo6
TitleHuman Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase 1A in complex with a consensus substrate peptide
Components
  • ARTIFICIAL CONSENSUS SEQUENCE
  • DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / TRANSFERASE PEPTIDE COMPLEX / SERINE/THREONINE-PROTEIN ATP-BINDING / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / DYRK1 / DYRK1A / KINASE / NUCLEUS / TRANSFERASE / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


ingression involved in gastrulation with mouth forming second / regulation of gastrulation / maintenance of epithelial cell apical/basal polarity / histone H3T45 kinase activity / circulatory system development / notochord formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / negative regulation of endopeptidase activity ...ingression involved in gastrulation with mouth forming second / regulation of gastrulation / maintenance of epithelial cell apical/basal polarity / histone H3T45 kinase activity / circulatory system development / notochord formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / positive regulation of BMP signaling pathway / establishment or maintenance of epithelial cell apical/basal polarity / dual-specificity kinase / [RNA-polymerase]-subunit kinase / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / mesoderm formation / G0 and Early G1 / positive regulation of epithelial to mesenchymal transition / somitogenesis / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / tau protein binding / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / membrane => GO:0016020 / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / apical plasma membrane / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / calcium ion binding / protein-containing complex binding / positive regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / 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-D15 / Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Protein crumbs homolog 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoos, A.K. / Soundararajan, M. / Elkins, J.M. / Fedorov, O. / Eswaran, J. / Phillips, C. / Pike, A.C.W. / Ugochukwu, E. / Muniz, J.R.C. / Burgess-Brown, N. ...Roos, A.K. / Soundararajan, M. / Elkins, J.M. / Fedorov, O. / Eswaran, J. / Phillips, C. / Pike, A.C.W. / Ugochukwu, E. / Muniz, J.R.C. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: Structure / Year: 2013
Title: Structures of Down Syndrome Kinases, Dyrks, Reveal Mechanisms of Kinase Activation and Substrate Recognition.
Authors: Soundararajan, M. / Roos, A.K. / Savitsky, P. / Filippakopoulos, P. / Kettenbach, A.N. / Olsen, J.V. / Gerber, S.A. / Eswaran, J. / Knapp, S. / Elkins, J.M.
History
DepositionJul 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 26, 2013Group: Database references / Derived calculations / Other
Revision 1.3Dec 4, 2013Group: Source and taxonomy
Revision 1.4Dec 21, 2016Group: Source and taxonomy
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_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: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
C: ARTIFICIAL CONSENSUS SEQUENCE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8216
Polymers89,8893
Non-polymers9313
Water4,900272
1
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
C: ARTIFICIAL CONSENSUS SEQUENCE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8194
Polymers45,3362
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-15.7 kcal/mol
Surface area15900 Å2
MethodPISA
2
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0012
Polymers44,5531
Non-polymers4481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.430, 168.430, 62.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILEAA146 - 19043 - 87
21ASPASPILEILEBB146 - 19043 - 87
12VALVALMETMETAA204 - 210101 - 107
22VALVALMETMETBB204 - 210101 - 107
13THRTHRSERSERAA215 - 242112 - 139
23THRTHRSERSERBB215 - 242112 - 139
14VALVALLYSLYSAA257 - 299154 - 196
24VALVALLYSLYSBB257 - 299154 - 196
15SERSERLEULEUAA301 - 314198 - 211
25SERSERLEULEUBB301 - 314198 - 211
16LEULEULYSLYSAA333 - 390230 - 287
26LEULEULYSLYSBB333 - 390230 - 287
17GLYGLYVALVALAA419 - 429316 - 326
27GLYGLYVALVALBB419 - 429316 - 326
18TYRTYRPHEPHEAA449 - 479346 - 376
28TYRTYRPHEPHEBB449 - 479346 - 376

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Components

#1: Protein DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A / PROTEIN KINASE MINIBRAIN HOMOLOG / HP86 / DUAL SPECIFICITY YAK1-RELATED KINASE / MNBH / HMNB


Mass: 44553.188 Da / Num. of mol.: 2 / Fragment: RESIDUES 127-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q13627, dual-specificity kinase
#2: Protein/peptide ARTIFICIAL CONSENSUS SEQUENCE


Mass: 782.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: Q5IJ48*PLUS
#3: Chemical ChemComp-D15 / N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide


Mass: 447.917 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22ClN5O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM FORMATE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.905
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.5→55.13 Å / Num. obs: 35283 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX3

2vx3


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.659 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1606 4.6 %RANDOM
Rwork0.188 ---
obs0.19 33667 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 65 272 5972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225844
X-RAY DIFFRACTIONr_bond_other_d0.0020.024063
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9817891
X-RAY DIFFRACTIONr_angle_other_deg139858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33323.623276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.894151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.041539
X-RAY DIFFRACTIONr_chiral_restr0.0910.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216399
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021228
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5091.53447
X-RAY DIFFRACTIONr_mcbond_other0.1511.51396
X-RAY DIFFRACTIONr_mcangle_it0.94225553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68632397
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6914.52338
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1400tight positional0.080.05
2B1400tight positional0.080.05
1A1843medium positional0.070.5
2B1843medium positional0.070.5
1A1400tight thermal0.140.5
2B1400tight thermal0.140.5
1A1843medium thermal0.142
2B1843medium thermal0.142
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 118 -
Rwork0.206 2448 -
obs--100 %
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)
14.0764-0.9842-0.79412.83760.05682.06870.0262-0.03840.08060.08130.0785-0.0797-0.0351-0.0038-0.10460.08110.0021-0.01780.0367-0.01050.0135-85.415232.6859.4469
20.53890.23760.25232.2150.03421.19490.0098-0.04390.02190.01060.03940.08080.0674-0.0478-0.04920.0223-0.00650.00710.0086-0.00150.0117-83.204412.2605-12.1071
33.0969-0.94990.21863.62960.30742.0497-0.0531-0.34370.0170.4326-0.10420.5492-0.2661-0.46210.15720.20960.01790.01430.2052-0.01840.1978-113.433529.1065-22.5713
42.02910.66340.33022.73530.54961.40170.06090.0666-0.289-0.0911-0.03250.3020.1319-0.198-0.02840.11380.0161-0.0720.069-0.00020.2357-114.94066.4646-41.0316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 241
2X-RAY DIFFRACTION2A242 - 481
3X-RAY DIFFRACTION3B133 - 241
4X-RAY DIFFRACTION4B242 - 481

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