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- PDB-3gp2: Calmodulin bound to peptide from calmodulin kinase II (CaMKII) -

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Basic information

Entry
Database: PDB / ID: 3gp2
TitleCalmodulin bound to peptide from calmodulin kinase II (CaMKII)
Components
  • Calcium/calmodulin-dependent protein kinase type II delta chain
  • Calmodulin
Keywordsmetal binding protein/Transferase / metal binding protein / kinase / ATP-binding / Calmodulin-binding / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / metal binding protein-Transferase complex
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / CH domain binding / 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 / regulation of the force of heart contraction ...regulation of relaxation of cardiac muscle / CH domain binding / 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 / regulation of the force of heart contraction / 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 / regulation of heart contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / relaxation of cardiac muscle / CaMK IV-mediated phosphorylation of CREB / myosin binding / regulation of cardiac muscle cell action potential / regulation of membrane depolarization / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle hypertrophy / 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 / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / cellular response to calcium ion / Ras activation upon Ca2+ influx through NMDA receptor / regulation of cell growth / peptidyl-threonine phosphorylation / RAF activation / sarcolemma / endocytic vesicle membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / disordered domain specific binding / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
Similarity search - Domain/homology
Calmodulin / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsNg, H.L. / Alber, T.A. / Wand, A.J.
CitationJournal: To be Published
Title: Calmodulin bound to peptide from calmodulin kinase II (CaMKII)
Authors: Ng, H.L. / Alber, T.A. / Wand, A.J.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: Calcium/calmodulin-dependent protein kinase type II delta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9446
Polymers18,7842
Non-polymers1604
Water3,603200
1
A: Calmodulin
B: Calcium/calmodulin-dependent protein kinase type II delta chain
hetero molecules

A: Calmodulin
B: Calcium/calmodulin-dependent protein kinase type II delta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,88812
Polymers37,5684
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8320 Å2
ΔGint-170 kcal/mol
Surface area16310 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-80 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.599, 38.409, 75.012
Angle α, β, γ (deg.)90.00, 125.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin / / CaM


Mass: 16592.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM, CAM, RCJMB04_24e7 / Production host: Escherichia coli (E. coli) / References: UniProt: P62149
#2: Protein/peptide Calcium/calmodulin-dependent protein kinase type II delta chain / CaM-kinase II delta chain / CaM kinase II subunit delta / CaMK-II subunit delta


Mass: 2191.664 Da / Num. of mol.: 1 / Fragment: residues 294-311 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.46→25.08 Å / Num. obs: 28224 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13
Reflection shellResolution: 1.46→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→25.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.503 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19218 1427 5.1 %RANDOM
Rwork0.15964 ---
obs0.16138 26767 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.52 Å2
2---0.05 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.46→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 4 200 1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221346
X-RAY DIFFRACTIONr_bond_other_d0.0010.02905
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9761802
X-RAY DIFFRACTIONr_angle_other_deg1.41332229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78426.16473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.671158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02249
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1191.5826
X-RAY DIFFRACTIONr_mcbond_other1.0311.5341
X-RAY DIFFRACTIONr_mcangle_it3.13921328
X-RAY DIFFRACTIONr_scbond_it4.3493520
X-RAY DIFFRACTIONr_scangle_it6.2644.5474
X-RAY DIFFRACTIONr_rigid_bond_restr2.15732251
X-RAY DIFFRACTIONr_sphericity_free11.0683205
X-RAY DIFFRACTIONr_sphericity_bonded5.56732238
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 95 -
Rwork0.383 1845 -
obs--100 %

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