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- PDB-3kk8: CaMKII Substrate Complex A -

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Basic information

Entry
Database: PDB / ID: 3kk8
TitleCaMKII Substrate Complex A
ComponentsCalcium/calmodulin dependent protein kinase II
KeywordsTRANSFERASE / Protein Kinase / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / medium-term memory / HSF1-dependent transactivation / Ca2+ pathway / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / axon cytoplasm ...Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / medium-term memory / HSF1-dependent transactivation / Ca2+ pathway / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / axon cytoplasm / MAPK cascade / perikaryon / transmembrane transporter binding / calmodulin binding / neuron projection / protein serine kinase activity / positive regulation of gene expression / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
Calcium/calmodulin-dependent protein kinase type II / Calcium/calmodulin-dependent protein kinase type II
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsKuriyan, J. / Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation.
Authors: Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H. / Kuriyan, J.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin dependent protein kinase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2282
Polymers32,2041
Non-polymers241
Water4,089227
1
A: Calcium/calmodulin dependent protein kinase II
hetero molecules

A: Calcium/calmodulin dependent protein kinase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4564
Polymers64,4072
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.361, 79.361, 175.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Calcium/calmodulin dependent protein kinase II


Mass: 32203.582 Da / Num. of mol.: 1 / Fragment: CaMKII kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-43, K11E8.1, K11E8.1d / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Q0, UniProt: O62305*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 15% 2-methyl-2,4-pentanediol, .1M potassium cholride, 5 mM magnesium sulfate, 50mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionRedundancy: 8.8 % / Number: 311357 / Rmerge(I) obs: 0.054 / Χ2: 1.04 / D res high: 1.72 Å / D res low: 50 Å / Num. obs: 35546 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.715098.910.0321.0338
2.943.7199.910.0441.0198.7
2.572.9410010.0551.0179.2
2.332.5710010.071.0339.3
2.172.3310010.0921.029.3
2.042.1710010.1271.0639.4
1.942.0410010.1871.0569.4
1.851.9410010.3191.0929.3
1.781.8510010.4771.0538.9
1.721.7898.510.5961.0276.1
ReflectionResolution: 1.72→68.729 Å / Num. all: 35546 / Num. obs: 35411 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rsym value: 0.054 / Net I/σ(I): 33.7
Reflection shellResolution: 1.72→1.78 Å / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.68 Å
Translation2.5 Å39.68 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→39.681 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU ML: 0.33 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1774 5.01 %RANDOM
Rwork0.178 ---
obs0.179 35408 99.63 %-
all-35546 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.561 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso max: 200.93 Å2 / Biso mean: 41.646 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.207 Å2-0 Å20 Å2
2--0.207 Å2-0 Å2
3----0.414 Å2
Refinement stepCycle: LAST / Resolution: 1.72→39.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 1 227 2495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014570
X-RAY DIFFRACTIONf_angle_d1.0968267
X-RAY DIFFRACTIONf_chiral_restr0.189345
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d14.9531136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.7660.2981330.2322494262798
1.766-1.8190.2431400.20625072647100
1.819-1.8770.2091520.19325202672100
1.877-1.9440.2231300.18325662696100
1.944-2.0220.2371230.16925652688100
2.022-2.1140.1741560.16725342690100
2.114-2.2260.2261250.16625652690100
2.226-2.3650.2321340.16625822716100
2.365-2.5480.2221390.16925812720100
2.548-2.8040.1971230.16826122735100
2.804-3.210.2061450.1726112756100
3.21-4.0430.1891370.16626852822100
4.043-39.6910.221370.1842812294998
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)
13.3036-0.83820.54290.7078-0.2901-0.63240.12010.7273-0.2731-0.5129-0.0716-0.05870.5840.399-0.06040.39530.03520.04550.39040.04680.20957.2322-51.52850.3438
21.1887-0.65330.01980.38281.17032.23290.08210.3516-0.1614-0.10150.0722-0.1030.3910.3196-0.13150.25550.02920.05070.33650.02080.240110.8435-48.5930.8381
31.69070.63670.23020.0671-0.06441.2096-0.26650.1425-0.57690.06850.1108-0.0329-0.02740.3590.13190.1965-0.04940.06210.28690.02630.28517.4784-37.92137.5171
42.6479-0.9205-1.63862.08790.61761.05270.0729-0.6774-0.10670.0674-0.0111-0.03330.21240.68590.08790.31070.15080.04170.40680.0820.245313.8755-49.39956.6431
50.55310.5345-0.31910.7025-0.29540.2325-0.01090.15430.0958-0.01680.02260.1342-0.0106-0.1351-0.03820.1983-0.01420.03330.25010.03020.19227.9913-28.3521.0801
60.7948-0.1572-0.4070.4717-0.54211.4207-0.21620.0816-0.16990.0670.0682-0.0094-0.1784-0.04330.13790.26030.01110.01890.20560.02750.207114.9775-29.14885.2203
71.37620.621-0.59940.5025-0.32320.95230.15080.05110.29260.04960.00140.0649-0.1644-0.0413-0.14520.21870.01590.05630.17050.05730.220717.1022-14.7467-3.0903
80.4716-1.0750.2924-0.50241.88320.1205-0.1007-0.0917-0.104-0.52970.37120.35230.54740.0658-0.11750.67470.05820.09221.37080.23440.5878-3.5206-12.932811.6504
91.5381-0.4021-0.63632.37930.84921.19050.0250.3478-0.2777-0.4361-0.09470.0756-0.1675-0.41370.06890.4309-0.0112-0.00510.4937-0.07750.4089-14.5466-28.147117.5189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:24)A7 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:53)A25 - 53
3X-RAY DIFFRACTION3(chain A and resid 54:73)A54 - 73
4X-RAY DIFFRACTION4(chain A and resid 74:83)A74 - 83
5X-RAY DIFFRACTION5(chain A and resid 84:145)A84 - 145
6X-RAY DIFFRACTION6(chain A and resid 146:167)A146 - 167
7X-RAY DIFFRACTION7(chain A and resid 168:270)A168 - 270
8X-RAY DIFFRACTION8(chain A and resid 271:275)A271 - 275
9X-RAY DIFFRACTION9(chain A and resid 276:289)A276 - 289

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