[English] 日本語
Yorodumi
- PDB-2wo6: Human Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase ... -

+
Open data


ID or keywords:

Loading...

-
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 / subapical complex / regulation of gastrulation / retinal cone cell development / maintenance of epithelial cell apical/basal polarity / histone H3T45 kinase activity / notochord formation / positive regulation of protein deacetylation / circulatory system development / peptidyl-serine autophosphorylation ...ingression involved in gastrulation with mouth forming second / subapical complex / regulation of gastrulation / retinal cone cell development / maintenance of epithelial cell apical/basal polarity / histone H3T45 kinase activity / notochord formation / positive regulation of protein deacetylation / circulatory system development / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / negative regulation of endopeptidase activity / apicolateral plasma membrane / aspartic-type endopeptidase inhibitor activity / positive regulation of BMP signaling pathway / establishment or maintenance of epithelial cell apical/basal polarity / photoreceptor cell maintenance / dual-specificity kinase / retina homeostasis / [RNA-polymerase]-subunit kinase / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of microtubule polymerization / tau-protein kinase activity / establishment of cell polarity / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / mesoderm formation / somitogenesis / positive regulation of epithelial to mesenchymal transition / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / visual perception / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / peptidyl-tyrosine phosphorylation / circadian rhythm / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / apical plasma membrane / ribonucleoprotein complex / protein phosphorylation / axon / 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-like domain ...: / 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-like domain / EGF-type aspartate/asparagine hydroxylation site / 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://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