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- PDB-2wel: Crystal structure of SU6656-bound calcium/calmodulin-dependent pr... -

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Basic information

Entry
Database: PDB / ID: 2wel
TitleCrystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin
Components
  • CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
  • CALMODULIN
KeywordsTRANSFERASE / CELLULAR DIFFERENTIATION / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOPROTEIN / CALMODULIN-BINDING / CALMODULIN BINDING / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / VASCULAR SMOOTH MUSCLE / SERINE-THREONINE KINASE
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / : / establishment of protein localization to mitochondrial membrane ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / : / establishment of protein localization to mitochondrial membrane / regulation of the force of heart contraction / type 3 metabotropic glutamate receptor binding / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of heart contraction / Calmodulin induced events / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / relaxation of cardiac muscle / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / response to corticosterone / regulation of membrane depolarization / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle hypertrophy / nitric-oxide synthase binding / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / HSF1-dependent transactivation / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / response to amphetamine / sarcoplasmic reticulum membrane / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity
Similarity search - Function
Helix Hairpins - #620 / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Helix Hairpins / NTF2-like domain superfamily / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site ...Helix Hairpins - #620 / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Helix Hairpins / NTF2-like domain superfamily / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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-K88 / PHOSPHATE ION / Calmodulin-1 / Calmodulin-3 / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPike, A.C.W. / Rellos, P. / Salah, E. / Burgess-Brown, N. / Keates, T. / Muniz, J. / Sethi, R. / Roos, A. / Filippakopoulos, P. / von Delft, F. ...Pike, A.C.W. / Rellos, P. / Salah, E. / Burgess-Brown, N. / Keates, T. / Muniz, J. / Sethi, R. / Roos, A. / Filippakopoulos, P. / von Delft, F. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Knapp, S.
CitationJournal: Plos Biol. / Year: 2010
Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation.
Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S.
History
DepositionMar 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Non-polymer description / Refinement description
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_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_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_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: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,04015
Polymers53,9462
Non-polymers1,09413
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-31.5 kcal/mol
Surface area28670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)68.260, 68.850, 121.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN / CALCIUM CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA / CAM-KINASE II DELTA CHAIN / CAM KINASE ...CALCIUM CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA / CAM-KINASE II DELTA CHAIN / CAM KINASE II SUBUNIT DELTA / CAMK-II SUBUNIT DELTA


Mass: 37006.500 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 11-335
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: Q13557, Ca2+/calmodulin-dependent protein kinase
#2: Protein CALMODULIN / / CAM


Mass: 16939.623 Da / Num. of mol.: 1
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: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 5 types, 418 molecules

#3: Chemical ChemComp-K88 / (3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE


Mass: 371.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(2-OXO-3-(4,5,6,7-TETRAHYDRO-1 H-INDOL-2-YLMETHYLENE)-2, 3-DIHYDRO-1H-INDOLE-5-SULFONIC ACID ...(2-OXO-3-(4,5,6,7-TETRAHYDRO-1 H-INDOL-2-YLMETHYLENE)-2, 3-DIHYDRO-1H-INDOLE-5-SULFONIC ACID DIMETHYLAMIDE) (K88): SU6656

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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: 2.6 Å3/Da / Density % sol: 52.72 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M SODIUM POTASSIUM PHOSPHATE, 20% PEG3350 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→33.13 Å / Num. obs: 45901 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.729 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / % 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 ENTRIES 2VN9, 1MXE

2vn9

1mxe


Resolution: 1.9→33.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.064 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19929 827 1.8 %RANDOM
Rwork0.16057 ---
obs0.1613 45074 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.066 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--1.02 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 64 405 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223702
X-RAY DIFFRACTIONr_bond_other_d0.0010.022529
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9734991
X-RAY DIFFRACTIONr_angle_other_deg0.9113.0016148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51824.59183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4031525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined0.2160.2755
X-RAY DIFFRACTIONr_nbd_other0.170.22422
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21791
X-RAY DIFFRACTIONr_nbtor_other0.0870.21772
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.230
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.30632233
X-RAY DIFFRACTIONr_mcbond_other1.1013909
X-RAY DIFFRACTIONr_mcangle_it4.70953596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0781469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.372111395
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
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 50 -
Rwork0.235 3286 -
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)
10.50990.0989-0.22620.4313-0.15341.74130.00210.01630.0196-0.04110.03830.036-0.0394-0.1191-0.04050.006-0.0012-0.00610.0226-0.00460.075917.2686-14.5916-13.2017
21.2733-0.57230.07132.76360.54651.26720.03050.2130.0167-0.34170.00740.1598-0.2259-0.0702-0.03790.11680.0058-0.0190.09360.04590.079788.1056-20.6549-51.1215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 276
2X-RAY DIFFRACTION2D3 - 147
3X-RAY DIFFRACTION2A294 - 316

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