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- PDB-5ig3: Crystal structure of the human CaMKII-alpha hub -

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Basic information

Entry
Database: PDB / ID: 5ig3
TitleCrystal structure of the human CaMKII-alpha hub
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase alpha / hub
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / negative regulation of hydrolase activity ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / negative regulation of hydrolase activity / Assembly and cell surface presentation of NMDA receptors / calmodulin-dependent protein kinase activity / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / regulation of neuronal synaptic plasticity / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle cell apoptotic process / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / G1/S transition of mitotic cell cycle / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to type II interferon / 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 / calcium ion transport / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / Ca2+ pathway / positive regulation of NF-kappaB transcription factor activity / kinase activity / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / dendritic spine / postsynaptic density / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / metal ion 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, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...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, / 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 / Alpha Beta
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMcSpadden, E. / Cao, Y.M. / Bhattacharyya, M. / Gee, C.L. / Barros, T. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NA United States
CitationJournal: Elife / Year: 2016
Title: Molecular mechanism of activation-triggered subunit exchange in Ca(2+)/calmodulin-dependent protein kinase II.
Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. ...Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. / Williams, E.R. / Kuriyan, J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Structure summary
Revision 1.2Jul 13, 2016Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha


Theoretical massNumber of molelcules
Total (without water)105,1246
Polymers105,1246
Non-polymers00
Water27015
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha

A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha


Theoretical massNumber of molelcules
Total (without water)210,24812
Polymers210,24812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area27640 Å2
ΔGint-221 kcal/mol
Surface area66900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.888, 89.888, 226.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Calcium/calmodulin-dependent protein kinase type II subunit alpha / / CaMK-II subunit alpha


Mass: 17520.680 Da / Num. of mol.: 6 / Fragment: UNP residues 345-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 35 % (v/v) MPD, 0.1 M HEPES pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2015 / Details: M1: parabola M2: torroid
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→48.64 Å / Num. obs: 25096 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 78 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 2.75→48.631 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.54
RfactorNum. reflection% reflection
Rfree0.2684 1184 4.71 %
Rwork0.22 --
obs0.2225 23820 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→48.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6297 0 0 15 6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026459
X-RAY DIFFRACTIONf_angle_d0.5058727
X-RAY DIFFRACTIONf_dihedral_angle_d11.4993798
X-RAY DIFFRACTIONf_chiral_restr0.042921
X-RAY DIFFRACTIONf_plane_restr0.0031131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8140.43631460.40932950X-RAY DIFFRACTION100
2.814-2.88430.36181020.33792969X-RAY DIFFRACTION100
2.8843-2.96230.36411240.30732914X-RAY DIFFRACTION100
2.9623-3.04950.33511540.28792909X-RAY DIFFRACTION100
3.0495-3.14790.3021600.2622930X-RAY DIFFRACTION100
3.1479-3.26040.3071530.24882910X-RAY DIFFRACTION100
3.2604-3.39090.33521320.26552910X-RAY DIFFRACTION100
3.3909-3.54520.36121240.24652977X-RAY DIFFRACTION100
3.5452-3.7320.30041450.2222945X-RAY DIFFRACTION100
3.732-3.96570.28041400.2032907X-RAY DIFFRACTION100
3.9657-4.27180.24211620.18452938X-RAY DIFFRACTION100
4.2718-4.70130.20271510.16542894X-RAY DIFFRACTION100
4.7013-5.38090.22221450.17452919X-RAY DIFFRACTION100
5.3809-6.77640.27371700.24392904X-RAY DIFFRACTION100
6.7764-48.63840.25081610.21662914X-RAY DIFFRACTION100
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)
14.3460.57620.80263.6227-2.0144.626-0.03420.3885-0.1134-0.6569-0.048-0.25420.15480.5510.04780.6364-0.04220.17660.6067-0.09590.5676-7.072875.2717-10.6222
23.68770.6597-0.41395.4568-1.01125.3146-0.02760.4719-0.42-0.7411-0.03120.08580.4074-0.16360.0390.69170.0791-0.05060.5191-0.0430.5444-55.085349.4096-27.8143
33.8488-1.73091.63024.3143-0.81916.06670.21550.0288-0.7827-0.67410.00570.35481.05980.0127-0.17510.80460.036-0.06250.46160.02180.6548-51.002924.3888-5.559
45.5725-0.0061.48124.8471-0.2243.73950.10720.2654-0.6975-0.3122-0.1248-0.33760.81250.60890.08020.68920.25130.03740.6674-0.00210.7338-24.725824.651815.0052
57.4790.62520.40261.44671.29984.1374-0.04440.89490.2399-0.8751-0.045-0.0139-1.04880.43950.07041.1827-0.0432-0.03780.65040.04750.5702-32.936475.3487-29.6994
64.156-0.2782-0.49645.0761-0.91691.8555-0.1455-0.6869-0.4616-0.2924-0.0542-1.13310.02061.29630.09540.52750.02780.06571.17710.0690.8518-2.004149.323812.868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 329 through 472)
2X-RAY DIFFRACTION2(chain 'B' and resid 344 through 473)
3X-RAY DIFFRACTION3(chain 'C' and resid 331 through 472)
4X-RAY DIFFRACTION4(chain 'D' and resid 331 through 473)
5X-RAY DIFFRACTION5(chain 'E' and resid 344 through 473)
6X-RAY DIFFRACTION6(chain 'F' and resid 344 through 472)

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