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- PDB-6of8: Structure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464Hi... -

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Basic information

Entry
Database: PDB / ID: 6of8
TitleStructure of Thr354Asn, Glu355Gln, Thr412Asn, Ile414Met, Ile464His, and Phe467Met mutant human CamKII-alpha hub domain
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsTRANSFERASE / CaMKII hub domain / SIGNALING PROTEIN
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: 2.1 Å
AuthorsMcSpadden, E.D. / Chi, C.C. / Gee, C.L. / Kuriyan, J.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)CHE -1609866 (ERW) United States
CitationJournal: Protein Sci. / Year: 2019
Title: Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/calmodulin-dependent protein kinase II.
Authors: McSpadden, E.D. / Xia, Z. / Chi, C.C. / Susa, A.C. / Shah, N.H. / Gee, C.L. / Williams, E.R. / Kuriyan, J.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 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
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,33315
Polymers108,8617
Non-polymers4728
Water1,892105
1
F: 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
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
hetero molecules

F: 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
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,66630
Polymers217,72214
Non-polymers94416
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area33980 Å2
ΔGint-237 kcal/mol
Surface area75450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.985, 121.343, 56.239
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15551.578 Da / Num. of mol.: 7 / Mutation: T354N, E355Q, T412N, I414M, I464H, F467M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 17 mg/mL mutant hub in 25 mM Tris, 150 mM KCl, 10% (v/v) glycerol, 2 mM DTT, 1 mM TCEP, pH 8.0 was mixed 1:1 with 235 mM K3Citrate, 15% (w/v) PEG 3350, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationMonochromator: S111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.1→47.76 Å / Num. obs: 60334 / % possible obs: 99.5 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Rrim(I) all: 0.047 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.150.8311.343240.640.5571.00396.7
9.39-47.760.0243.76910.930.0140.02598.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 2.1→47.505 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 3071 5.09 %
Rwork0.2217 --
obs0.2236 60303 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7358 0 23 105 7486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027569
X-RAY DIFFRACTIONf_angle_d0.51110217
X-RAY DIFFRACTIONf_dihedral_angle_d18.3444477
X-RAY DIFFRACTIONf_chiral_restr0.0421043
X-RAY DIFFRACTIONf_plane_restr0.0031339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.37831420.34872526X-RAY DIFFRACTION98
2.1328-2.16780.35881270.31922632X-RAY DIFFRACTION100
2.1678-2.20520.3071290.30662598X-RAY DIFFRACTION100
2.2052-2.24530.37381410.30712592X-RAY DIFFRACTION99
2.2453-2.28840.34781490.3062561X-RAY DIFFRACTION99
2.2884-2.33520.32311550.29722556X-RAY DIFFRACTION99
2.3352-2.38590.30431420.27832593X-RAY DIFFRACTION100
2.3859-2.44140.32771370.27242618X-RAY DIFFRACTION100
2.4414-2.50250.28121280.26832592X-RAY DIFFRACTION100
2.5025-2.57010.32141550.28862605X-RAY DIFFRACTION100
2.5701-2.64580.27631310.27352596X-RAY DIFFRACTION100
2.6458-2.73110.33951460.28222597X-RAY DIFFRACTION99
2.7311-2.82880.29361480.27192595X-RAY DIFFRACTION99
2.8288-2.9420.28521550.25542573X-RAY DIFFRACTION100
2.942-3.07590.27431400.24992603X-RAY DIFFRACTION100
3.0759-3.2380.2891470.23822591X-RAY DIFFRACTION100
3.238-3.44080.23191220.21972656X-RAY DIFFRACTION100
3.4408-3.70640.24991130.20822637X-RAY DIFFRACTION100
3.7064-4.07920.22981400.19522618X-RAY DIFFRACTION100
4.0792-4.6690.21971280.1822633X-RAY DIFFRACTION100
4.669-5.88070.21391420.18372621X-RAY DIFFRACTION100
5.8807-47.51670.24521540.1962639X-RAY DIFFRACTION99

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