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- PDB-5fg8: Drosophila CaMKII-wt in complex with a fragment of the Eag potass... -

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Basic information

Entry
Database: PDB / ID: 5fg8
TitleDrosophila CaMKII-wt in complex with a fragment of the Eag potassium channel and Mg2+/ADP
Components
  • Calcium/calmodulin-dependent protein kinase type II alpha chain
  • Potassium voltage-gated channel protein eag
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 / HSF1-dependent transactivation / RAF activation / Ion homeostasis / positive regulation of synaptic transmission, dopaminergic / 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 / HSF1-dependent transactivation / RAF activation / Ion homeostasis / positive regulation of synaptic transmission, dopaminergic / 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 / male courtship behavior / Ca2+/calmodulin-dependent protein kinase / regulation of filopodium assembly / voltage-gated monoatomic cation channel activity / calcium/calmodulin-dependent protein kinase activity / negative regulation of cytokine production / regulation of heart contraction / neuromuscular junction development / presynaptic active zone / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / voltage-gated potassium channel activity / long-term memory / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to starvation / regulation of membrane potential / learning / potassium ion transport / sensory perception of smell / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / learning or memory / calmodulin binding / neuron projection / axon / 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 domain / PAS-associated, C-terminal / PAC domain profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...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 domain / PAS-associated, C-terminal / 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
ADENOSINE-5'-DIPHOSPHATE / 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: 1.955 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 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Nov 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 1.3May 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 type II alpha chain
B: Potassium voltage-gated channel protein eag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2266
Polymers37,5912
Non-polymers6364
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.503, 59.223, 70.759
Angle α, β, γ (deg.)90.000, 97.230, 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 type II alpha chain / CaM-kinase II alpha chain


Mass: 32181.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Constitutively active CaMKII kinase domain construct
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CaMKII, CaM, CG18069 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q00168, Ca2+/calmodulin-dependent protein kinase
#2: Protein Potassium voltage-gated channel protein eag / Ether-a-go-go protein


Mass: 5408.918 Da / Num. of mol.: 1
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, 69 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 26% w/v PEG 4000, 0.2 M ammonium acetate, 5 mM magnesium chloride, 0.8 mM ADP, 0.1 mM 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: 0.98403 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98403 Å / Relative weight: 1
ReflectionResolution: 1.88→30.194 Å / Num. all: 23764 / Num. obs: 23764 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 35.65 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Rsym value: 0.05 / Net I/av σ(I): 8.702 / Net I/σ(I): 12.4 / Num. measured all: 77000
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.88-1.952.40.6811.1511120990.520.6811.588
1.95-2.022.90.4241.8657422330.2960.4242.596.9
2.02-2.13.40.2822.7762122160.1790.2824.299.4
2.1-2.23.40.2083.6731021290.1330.2085.599.7
2.2-2.33.40.1584.7688920240.1010.1586.999.4
2.3-2.433.40.1166.4668819460.0740.1168.999.7
2.43-2.573.40.0898.2619918160.0570.08910.599.4
2.57-2.753.40.06610.6574516960.0420.06613.799.4
2.75-2.973.40.05112.7543916080.0320.05117.799.4
2.97-3.263.30.04414.5489514650.0280.0442299.3
3.26-3.643.30.03716.1445013380.0240.03726.497.7
3.64-4.23.30.03715.9378811510.0240.03729.697.9
4.2-5.153.10.03816.931189900.0260.03830.297.6
5.15-7.283.10.03318.424147730.0220.03329.596.7
7.28-30.1942.70.033187592800.0240.0332863.7

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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: 1.955→30.194 Å / FOM work R set: 0.7871 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1096 5.14 %random selection
Rwork0.1909 20232 --
obs0.1924 21328 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.22 Å2 / Biso mean: 57.66 Å2 / Biso min: 16.04 Å2
Refinement stepCycle: final / Resolution: 1.955→30.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 40 69 2380
Biso mean--60.08 45.3 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012410
X-RAY DIFFRACTIONf_angle_d1.1713282
X-RAY DIFFRACTIONf_chiral_restr0.069352
X-RAY DIFFRACTIONf_plane_restr0.005418
X-RAY DIFFRACTIONf_dihedral_angle_d16.492894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9553-2.04430.30311470.29862538268598
2.0443-2.15210.3571350.266225332668100
2.1521-2.28690.26981290.24242569269899
2.2869-2.46340.22911160.22412566268299
2.4634-2.71110.25291460.22352518266498
2.7111-3.10310.24141560.20152552270899
3.1031-3.90820.19851470.1762518266598
3.9082-30.19730.17911200.15272438255892
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)
17.1881.97910.62387.19954.14824.9130.34530.29740.15960.6098-0.254-1.1692-0.5190.6757-0.02210.59640.0193-0.0560.50250.2090.53998.77566.36052.2287
20.7189-0.16890.10136.13141.1667.0303-0.0459-0.2022-0.18760.8055-0.46160.02240.1861-0.06910.41480.2297-0.06050.08680.36960.00980.4033-0.090310.585-9.0173
32.25871.5409-0.89057.68960.93276.914-0.17860.05860.0033-1.3117-0.34990.8012-0.4006-0.70390.28540.33080.109-0.14020.2943-0.07810.374-4.638812.9177-26.2448
46.7597-2.0803-2.53134.96314.16099.20110.041-0.4194-0.0856-0.67690.1777-1.5249-0.64560.8448-0.44010.3786-0.11130.02830.39920.14010.45867.092717.4417-21.5072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 129 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 275 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 780 through 794 )B0

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