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- PDB-3soa: Full-length human CaMKII -

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Basic information

Entry
Database: PDB / ID: 3soa
TitleFull-length human CaMKII
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha with a beta 7 linker
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / Protein Kinase / Phosphorylation / Calcium/calmodulin / cytosolic / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / positive regulation of calcium ion transport ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / Trafficking of AMPA receptors / positive regulation of calcium ion transport / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / regulation of neuronal synaptic plasticity / Long-term potentiation / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / regulation of protein localization to plasma membrane / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / cellular response to type II interferon / long-term synaptic potentiation / G1/S transition of mitotic cell cycle / Interferon gamma signaling / 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 / calcium ion transport / positive regulation of NF-kappaB transcription factor activity / kinase activity / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / Ca2+ pathway / RAF/MAP kinase cascade / dendritic spine / calmodulin binding / neuron projection / postsynaptic density / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / 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 / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / 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-DB8 / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5501 Å
AuthorsChao, L.H. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca(2+)/Calmodulin- Dependent Kinase II Holoenzyme.
Authors: Chao, L.H. / Stratton, M.M. / Lee, I.H. / Rosenberg, O.S. / Levitz, J. / Mandell, D.J. / Kortemme, T. / Groves, J.T. / Schulman, H. / Kuriyan, J.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Non-polymer description / Structure summary
Revision 1.2Sep 14, 2011Group: Database references / Structure summary
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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 subunit alpha with a beta 7 linker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1762
Polymers50,6461
Non-polymers5301
Water00
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha with a beta 7 linker
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)614,11724
Polymers607,75212
Non-polymers6,36512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation11_555-x+y,y,-z1
crystal symmetry operation12_555x,x-y,-z1
Buried area49920 Å2
ΔGint-202 kcal/mol
Surface area219970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.720, 155.720, 106.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type II subunit alpha with a beta 7 linker / CaM kinase II subunit alpha / CaMK-II subunit alpha / CaM kinase II subunit beta 7 / CaMK-II subunit beta 7


Mass: 50646.004 Da / Num. of mol.: 1 / Mutation: K42M, D135N, T306V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: camk2a, camka, kiaa0968, camk2b, camkb / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-DB8 / 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile / Bosutinib


Mass: 530.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3 / Comment: inhibitor, medication*YM

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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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion / pH: 5.5
Details: 1.2 M Ammonium Tartrate, 100 mM bistrispropane, pH 5.5, VAPOR DIFFUSION, temperature 288.15K

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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: Jul 14, 2010
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
ReflectionResolution: 3.55→50 Å / Num. all: 9966 / Num. obs: 8555 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.55→3.73 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VN9 AND 2UX0

2vn9

2ux0


Resolution: 3.5501→45.949 Å / SU ML: 1.14 / σ(F): 0 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3271 856 10.01 %
Rwork0.2731 --
obs0.2785 8551 88.78 %
all-9966 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 133.447 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1555 Å20 Å2-0 Å2
2--5.1555 Å20 Å2
3----10.311 Å2
Refinement stepCycle: LAST / Resolution: 3.5501→45.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 36 0 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083629
X-RAY DIFFRACTIONf_angle_d1.4944912
X-RAY DIFFRACTIONf_dihedral_angle_d15.2851350
X-RAY DIFFRACTIONf_chiral_restr0.091527
X-RAY DIFFRACTIONf_plane_restr0.005627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5501-3.77240.3251720.3508654X-RAY DIFFRACTION46
3.7724-4.06350.41841390.34461248X-RAY DIFFRACTION90
4.0635-4.47220.32731570.30951410X-RAY DIFFRACTION99
4.4722-5.11860.32341570.25351416X-RAY DIFFRACTION99
5.1186-6.4460.43441610.31561450X-RAY DIFFRACTION99
6.446-45.95320.25551700.21711517X-RAY DIFFRACTION97
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)
12.5541-2.51270.95582.77611.12824.1605-0.039-0.751-0.78070.7620.64730.84580.4881-1.1428-0.52380.8222-0.14780.29431.22780.45821.4781-48.16012.911732.1022
23.35070.89-0.45017.68672.12131.2699-0.6227-1.04340.06710.42010.47412.867-0.2961-0.68320.19891.0561-0.18480.52152.24540.34342.1827-67.53621.348330.8161
34.22441.875-3.38258.35591.83986.32260.2208-0.64381.03951.0495-0.10880.9510.724-0.5380.02370.7664-0.0812-0.04610.75290.26870.795-32.7545-13.021312.0971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:261)
2X-RAY DIFFRACTION2(chain A and resid 262:292)
3X-RAY DIFFRACTION3(chain A and resid 293:435)

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