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- PDB-2vd5: Structure of Human Myotonic Dystrophy Protein Kinase in Complex w... -

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Basic information

Entry
Database: PDB / ID: 2vd5
TitleStructure of Human Myotonic Dystrophy Protein Kinase in Complex with the Bisindoylmaleide inhibitor BIM VIII
ComponentsDMPK PROTEIN
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / CARDIAC CONTRACTILITY / MUSCLE DIFFERENTIATION
Function / homology
Function and homology information


regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction / regulation of skeletal muscle contraction by calcium ion signaling / muscle cell apoptotic process / regulation of myotube differentiation / myosin phosphatase regulator activity / regulation of synapse structural plasticity / nuclear envelope organization / regulation of heart contraction / nuclear outer membrane / regulation of sodium ion transport ...regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction / regulation of skeletal muscle contraction by calcium ion signaling / muscle cell apoptotic process / regulation of myotube differentiation / myosin phosphatase regulator activity / regulation of synapse structural plasticity / nuclear envelope organization / regulation of heart contraction / nuclear outer membrane / regulation of sodium ion transport / Ion homeostasis / sarcoplasmic reticulum membrane / intracellular calcium ion homeostasis / nuclear membrane / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / : / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / : / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Chem-BI8 / Myotonin-protein kinase / Myotonin-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPike, A.C.W. / Amos, A. / Elkins, J. / Bullock, A. / Guo, K. / Fedorov, O. / Bunkoczi, G. / Filippakopoulos, P. / Pilka, E.S. / Ugochukwu, E. ...Pike, A.C.W. / Amos, A. / Elkins, J. / Bullock, A. / Guo, K. / Fedorov, O. / Bunkoczi, G. / Filippakopoulos, P. / Pilka, E.S. / Ugochukwu, E. / Umeano, C. / Niesen, F. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / von Delft, F. / Knapp, S.
CitationJournal: Protein Sci. / Year: 2009
Title: Structure of Dystrophia Myotonica Protein Kinase.
Authors: Elkins, J. / Amos, A. / Niesen, F. / Pike, A.C.W. / Fedorov, O. / Knapp, S.
History
DepositionSep 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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_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_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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DMPK PROTEIN
B: DMPK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0084
Polymers92,2112
Non-polymers7972
Water1629
1
A: DMPK PROTEIN
hetero molecules

A: DMPK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0084
Polymers92,2112
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area2900 Å2
ΔGint-41.3 kcal/mol
Surface area41930 Å2
MethodPQS
2
B: DMPK PROTEIN
hetero molecules

B: DMPK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0084
Polymers92,2112
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2520 Å2
ΔGint-37.1 kcal/mol
Surface area41250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)122.599, 122.599, 134.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUAA11 - 1603 - 152
21GLNGLNLEULEUBB11 - 1603 - 152
12ALAALAGLYGLYAA169 - 247161 - 239
22ALAALAGLYGLYBB169 - 247161 - 239
13GLYGLYLEULEUAA253 - 299245 - 291
23GLYGLYLEULEUBB253 - 299245 - 291
14VALVALGLYGLYAA306 - 329298 - 321
24VALVALGLYGLYBB306 - 329298 - 321
15PHEPHEASPASPAA338 - 357330 - 349
25PHEPHEASPASPBB338 - 357330 - 349
16GLYGLYVALVALAA395 - 415387 - 407
26GLYGLYVALVALBB395 - 415387 - 407
17SERSERPROPROAA161 - 168153 - 160
27SERSERPROPROBB161 - 168153 - 160
18ALAALAPROPROAA330 - 337322 - 329
28ALAALAPROPROBB330 - 337322 - 329

NCS oper: (Code: given
Matrix: (-0.41758, -0.33594, -0.84426), (0.32662, 0.81155, -0.48447), (0.84791, -0.47806, -0.22916)
Vector: 59.35064, -54.20861, -58.52479)

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Components

#1: Protein DMPK PROTEIN / MYOTONIC DYSTROPHY PROTEIN KINASE


Mass: 46105.363 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 11-420
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: Q6P5Z6, UniProt: Q09013*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-BI8 / 3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1-METHYL-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE


Mass: 398.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBISINDOLYLMALEIMIDE VIII (BM8): BIM8

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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: 3.16 Å3/Da / Density % sol: 61.13 % / Description: NONE
Crystal growpH: 7
Details: 1M AMMONIUM SULPHATE, 1.5% PEG 3350, 0.1M BIS-TRIS PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006029
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006029 Å / Relative weight: 1
ReflectionResolution: 2.8→45.27 Å / Num. obs: 29215 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 74.94 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESM

2esm


Resolution: 2.8→41.24 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.525 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.652 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1262 4.3 %RANDOM
Rwork0.196 ---
obs0.198 27921 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5831 0 60 9 5900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226046
X-RAY DIFFRACTIONr_bond_other_d0.0010.023984
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9748216
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0019592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86222.908251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32815876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.911536
X-RAY DIFFRACTIONr_chiral_restr0.0670.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021305
X-RAY DIFFRACTIONr_nbd_refined0.2220.21310
X-RAY DIFFRACTIONr_nbd_other0.1840.23935
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22997
X-RAY DIFFRACTIONr_nbtor_other0.0880.23042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65133875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.75156016
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.61782527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.441112200
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4521 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal0.612
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 75
Rwork0.273 2039
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)
13.3903-0.76180.44422.0778-0.32581.5685-0.0091-0.0271-0.09670.00910.0464-0.2902-0.0645-0.0655-0.0373-0.2948-0.01920.0213-0.20080.0267-0.244166.4844-44.581210.7946
22.2010.1337-0.453.4397-1.52693.1851-0.29570.2177-0.35860.20850.1678-0.02650.41630.20010.1279-0.17490.05790.0354-0.1031-0.1311-0.172537.2659-73.699916.6999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 416
2X-RAY DIFFRACTION2B11 - 416

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