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- PDB-5h9b: Drosophila CaMKII-wt in complex with a fragment of the Eag potass... -

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Basic information

Entry
Database: PDB / ID: 5h9b
TitleDrosophila CaMKII-wt in complex with a fragment of the Eag potassium channel and Mg2+/AMPPN
Components
  • Calcium/calmodulin-dependent protein kinase II, isoform C
  • Potassium voltage-gated channel protein eagVoltage-gated potassium channel
KeywordsTRANSFERASE / protein kinase / potassium channel / complex
Function / homology
Function and homology information


perineurial glial growth / regulation of ovulation / Ca2+ pathway / Ion transport by P-type ATPases / RAF activation / positive regulation of synaptic transmission, dopaminergic / HSF1-dependent transactivation / Ion homeostasis / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to ether ...perineurial glial growth / regulation of ovulation / Ca2+ pathway / Ion transport by P-type ATPases / RAF activation / positive regulation of synaptic transmission, dopaminergic / HSF1-dependent transactivation / Ion homeostasis / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to ether / Voltage gated Potassium channels / courtship behavior / regulation of synaptic assembly at neuromuscular junction / peptidyl-threonine autophosphorylation / protein serine/threonine kinase activity => GO:0004674 / male courtship behavior / Ca2+/calmodulin-dependent protein kinase / regulation of filopodium assembly / voltage-gated monoatomic cation channel activity / regulation of heart contraction / calmodulin-dependent protein kinase activity / negative regulation of cytokine production / neuromuscular junction development / presynaptic active zone / voltage-gated potassium channel activity / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / long-term memory / potassium ion transmembrane transport / voltage-gated potassium channel complex / cellular response to starvation / learning / regulation of membrane potential / potassium ion transport / sensory perception of smell / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / learning or memory / calmodulin binding / neuron projection / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage-dependent, EAG / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel, voltage-dependent, EAG / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / NTF2-like domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 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
AMP PHOSPHORAMIDATE / Calcium/calmodulin-dependent protein kinase / Calcium/calmodulin-dependent protein kinase type II alpha chain / Potassium voltage-gated channel protein eag
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsCastro-Rodrigues, A.F. / Morais-Cabral, J.H.
CitationJournal: J.Mol.Biol. / Year: 2018
Title: The Interaction between the Drosophila EAG Potassium Channel and the Protein Kinase CaMKII Involves an Extensive Interface at the Active Site of the Kinase.
Authors: Castro-Rodrigues, A.F. / Zhao, Y. / Fonseca, F. / Gabant, G. / Cadene, M. / Robertson, G.A. / Morais-Cabral, J.H.
History
DepositionDec 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 II, isoform C
B: Potassium voltage-gated channel protein eag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1335
Polymers37,5912
Non-polymers5433
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-19 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.823, 59.127, 70.339
Angle α, β, γ (deg.)90.000, 99.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Calcium/calmodulin-dependent protein kinase II, isoform C / Calcium/calmodulin-dependent protein kinase type II alpha chain / Calcium/calmodulin-dependent ...Calcium/calmodulin-dependent protein kinase type II alpha chain / Calcium/calmodulin-dependent protein kinase II / isoform H / FI03620p


Mass: 32181.668 Da / Num. of mol.: 1 / Fragment: UNP residues 1-283
Source method: isolated from a genetically manipulated source
Details: Constitutively active CaMKII kinase domain construct
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CaMKII, CaMKII-RA, CG18069, Dmel_CG18069 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A4V133, UniProt: Q00168*PLUS, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, Ca2+/calmodulin-dependent protein kinase
#2: Protein Potassium voltage-gated channel protein eag / Voltage-gated potassium channel / Ether-a-go-go protein


Mass: 5408.918 Da / Num. of mol.: 1 / Fragment: UNP residues 770-820
Source method: isolated from a genetically manipulated source
Details: Eag construct including the CaMKII-binding motif / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: eag, CG10952 / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: Q02280

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Non-polymers , 4 types, 25 molecules

#3: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 26% PEG 4000, 0.2 M ammonium acetate, 5 mM magnesium chloride, 0.8 mM AMPPNP, 0.1 M sodium citrate pH 5.0
PH range: 5.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98406 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98406 Å / Relative weight: 1
ReflectionResolution: 2.25→45.026 Å / Num. all: 13806 / Num. obs: 13806 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.28 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Rsym value: 0.067 / Net I/av σ(I): 7.475 / Net I/σ(I): 10.4 / Num. measured all: 47277
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.25-2.333.50.7930.9468613420.4990.7931.799.5
2.33-2.423.50.5461.4450313000.3460.5462.499.5
2.42-2.523.50.4781.6435912440.3010.4782.799.7
2.52-2.633.50.3542.1420112100.2220.3543.599.2
2.63-2.763.50.2393.1398911510.1510.2394.699.5
2.76-2.93.50.1644.5379810820.1030.1646.499.6
2.9-3.083.50.1146.5363410520.0720.1148.699.7
3.08-3.293.40.0838.534119910.0520.08311.799.8
3.29-3.563.40.06310.230769080.040.06315.599.7
3.56-3.93.30.0512.827788330.0320.0519.699
3.9-4.363.30.04512.824807570.0280.0452399.2
4.36-5.033.30.0414.221556600.0260.0425.497.8
5.03-6.163.30.04214.319175770.0260.04224.299
6.16-8.713.40.03515.715094480.0230.03527.699.2
8.71-45.0263.10.03116.97812510.0210.03128.498.2

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→45.026 Å / FOM work R set: 0.7336 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 689 5 %
Rwork0.2029 13091 -
obs0.2039 13780 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.01 Å2 / Biso mean: 75.6 Å2 / Biso min: 33.73 Å2
Refinement stepCycle: final / Resolution: 2.25→45.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 34 22 2344
Biso mean--71.99 48.77 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042382
X-RAY DIFFRACTIONf_angle_d0.7583237
X-RAY DIFFRACTIONf_chiral_restr0.047346
X-RAY DIFFRACTIONf_plane_restr0.003414
X-RAY DIFFRACTIONf_dihedral_angle_d15.612872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.42380.37791520.32222585273799
2.4238-2.66770.33341280.28922603273199
2.6677-3.05360.29111300.23512629275999
3.0536-3.84690.21931270.20842641276899
3.8469-45.03530.17371520.15872633278598
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)
15.7592.84491.10933.73542.76874.5541-0.06320.3591-0.0020.4102-0.1643-0.98530.41380.75290.21581.060.01580.04720.62430.2110.749.40088.89811.5349
22.17930.24990.42836.89162.78588.61550.0288-0.4392-0.06741.0476-0.39420.20770.2431-0.1420.3580.6191-0.04920.15810.43970.0620.4931-1.159.9387-9.9412
33.04951.84440.40496.30590.48948.5204-0.0236-0.2651-0.23851.1672-0.1570.99230.0581-0.59270.19920.57640.04830.12860.3810.0030.496-3.623612.7504-14.6812
41.85230.8561-0.86898.03470.24694.8335-0.12760.25440.0264-1.8092-0.25530.6784-0.5275-0.5270.31130.91050.1356-0.1450.4078-0.04760.4655-3.656612.6998-30.1622
51.8206-1.6722-2.43191.52342.20453.4255-0.0830.0502-0.9072-0.26731.1490.15320.77370.8169-0.89510.7084-0.00710.16820.5192-0.06820.91169.42374.54-31.0961
69.631-1.7903-1.26479.88645.59958.69650.4158-0.7794-1.8084-0.0214-0.0696-1.08340.20470.5552-0.21550.5837-0.02850.03190.58480.06850.93929.859313.0954-20.0945
73.509-2.81072.35233.9224-0.00873.71930.2496-1.08340.4884-0.7462-0.2016-0.8267-1.5125-0.4868-0.23931.1675-0.18240.05520.8231-0.04430.49896.418928.0607-17.7295
88.8229-6.5846-8.79849.91435.93878.85440.3971-0.68810.7971-1.1873-0.5515-0.0847-1.1905-0.39110.03442.03870.05780.11731.2878-0.39920.6189-1.291236.3165-16.8087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 51 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 129 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 170 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 275 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 779 through 783 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 784 through 788 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 789 through 793 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 794 through 795 )B0

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