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- PDB-2a2a: High-resolution crystallographic analysis of the autoinhibited co... -

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Basic information

Entry
Database: PDB / ID: 2a2a
TitleHigh-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated protein kinase
ComponentsDeath-associated protein kinase 2
KeywordsTRANSFERASE / protein kinase / autoinhibition
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / anoikis / positive regulation of neutrophil chemotaxis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / anoikis / positive regulation of neutrophil chemotaxis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / regulation of autophagy / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / apoptotic process / Golgi apparatus / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. ...Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKursula, P. / Wilmanns, M.
CitationJournal: Structure / Year: 2016
Title: Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites
Authors: Simon, B. / Huart, A.S. / Temmerman, K. / Vahokoski, J. / Mertens, H.D. / Komadina, D. / Hoffmann, J.E. / Yumerefendi, H. / Svergun, D.I. / Kursula, P. / Schultz, C. / McCarthy, A.A. / Hart, D.J. / Wilmanns, M.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death-associated protein kinase 2
B: Death-associated protein kinase 2
C: Death-associated protein kinase 2
D: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,85022
Polymers148,6664
Non-polymers1,18418
Water24,6991371
1
A: Death-associated protein kinase 2
B: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,89611
Polymers74,3332
Non-polymers5639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-73 kcal/mol
Surface area27660 Å2
MethodPISA
2
C: Death-associated protein kinase 2
D: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,95311
Polymers74,3332
Non-polymers6209
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-64 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.300, 60.650, 98.710
Angle α, β, γ (deg.)92.16, 103.45, 94.25
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Death-associated protein kinase 2 / DRP-1 kinase / DAP kinase 2 / DAP- kinase related protein 1 / DRP-1


Mass: 37166.504 Da / Num. of mol.: 4 / Fragment: D40 truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9UIK4, EC: 2.7.1.37

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Non-polymers , 5 types, 1389 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThere are differences between the seqres and the sequence database. The depositors say that there ...There are differences between the seqres and the sequence database. The depositors say that there are two versions of the sequence in the databases and the sequence in this protein corresponds to the other one and is thus correct. The difference is evidenced in the REFERENCE: JOURNAL Mol. Cell. Biol. 20 (3), 1044-1054 (2000) PUBMED 10629061

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, glycerol, DTT, Tris, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9206 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9206 Å / Relative weight: 1
ReflectionResolution: 1.47→40 Å / Num. all: 200389 / Num. obs: 200389 / % possible obs: 94.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.049 / Net I/σ(I): 11.1
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 18844 / Rsym value: 0.424 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A27

2a27


Resolution: 1.47→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.59 / SU ML: 0.061 / Isotropic thermal model: ANISOTROPIC REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20688 2003 1 %RANDOM
Rwork0.14959 ---
all0.15016 200335 --
obs0.15016 200335 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0.24 Å21.01 Å2
2--0.36 Å2-0.2 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.47→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9884 0 61 1371 11316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210391
X-RAY DIFFRACTIONr_bond_other_d0.0020.029549
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.96514051
X-RAY DIFFRACTIONr_angle_other_deg0.873322275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93451268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94724.231520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.953151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9671576
X-RAY DIFFRACTIONr_chiral_restr0.1070.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022132
X-RAY DIFFRACTIONr_nbd_refined0.2330.22239
X-RAY DIFFRACTIONr_nbd_other0.1880.29844
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25075
X-RAY DIFFRACTIONr_nbtor_other0.0850.25779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2943
X-RAY DIFFRACTIONr_metal_ion_refined0.2150.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.248
X-RAY DIFFRACTIONr_mcbond_it4.10226223
X-RAY DIFFRACTIONr_mcbond_other2.06122514
X-RAY DIFFRACTIONr_mcangle_it5.22310154
X-RAY DIFFRACTIONr_scbond_it6.9084.54233
X-RAY DIFFRACTIONr_scangle_it9.18763897
X-RAY DIFFRACTIONr_rigid_bond_restr3.578320463
X-RAY DIFFRACTIONr_sphericity_free14.7331382
X-RAY DIFFRACTIONr_sphericity_bonded5.875319726
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 144 -
Rwork0.194 14303 -
obs--93.16 %

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