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- PDB-2v7o: Crystal structure of human calcium-calmodulin-dependent protein k... -

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Basic information

Entry
Database: PDB / ID: 2v7o
TitleCrystal structure of human calcium-calmodulin-dependent protein kinase II gamma
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN
KeywordsTRANSFERASE / KINASE / S/T KINASE / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / CALMODULIN-BINDING
Function / homology
Function and homology information


regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB ...regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / regulation of neuron projection development / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of calcium ion transport / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / regulation of neuronal synaptic plasticity / HSF1-dependent transactivation / regulation of protein localization to plasma membrane / Ion homeostasis / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / RAF activation / long-term synaptic potentiation / 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 / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / nervous system development / RAF/MAP kinase cascade / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein serine kinase activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 / 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
BISINDOLYLMALEIMIDE IX / Calcium/calmodulin-dependent protein kinase type II subunit gamma / Calcium/calmodulin-dependent protein kinase type II subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Shrestha, L. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Edwards, A. / Weigelt, J. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Shrestha, L. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S.
CitationJournal: Plos Biol. / Year: 2010
Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation.
Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S.
History
DepositionJul 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0844
Polymers38,5021
Non-polymers5823
Water1,982110
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.703, 117.226, 75.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2030-

HOH

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Components

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN / CAM-KINASE II GAMMA CHAIN / CAM KINASE II GAMMA SUBUNIT / CAMK-II SUBUNIT GAMMA / CALCIUM- ...CAM-KINASE II GAMMA CHAIN / CAM KINASE II GAMMA SUBUNIT / CAMK-II SUBUNIT GAMMA / CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASE II GAMMA


Mass: 38501.922 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 5-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) ROSETTA / Variant (production host): R3
References: UniProt: Q8N4I3, UniProt: Q13555*PLUS, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-DRN / BISINDOLYLMALEIMIDE IX


Mass: 457.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23N5O2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBISINDOLYLMALEIMIDE IX (DRN): BIM-9

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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: 2.59 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 7
Details: 0.10M MAGNESIUM CHLORIDE, 0.1M HEPES PH7, 20% PEG6K, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00721
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00721 Å / Relative weight: 1
ReflectionResolution: 2.25→42.33 Å / Num. obs: 18326 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BDW

1bdw


Resolution: 2.25→35.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.48 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 936 5.1 %RANDOM
Rwork0.176 ---
obs0.179 17388 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.43 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 41 110 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212524
X-RAY DIFFRACTIONr_bond_other_d0.0010.021706
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9633424
X-RAY DIFFRACTIONr_angle_other_deg1.333.0034123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40423.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65315.036415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_nbd_refined0.190.2458
X-RAY DIFFRACTIONr_nbd_other0.180.21718
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21192
X-RAY DIFFRACTIONr_nbtor_other0.0890.21267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 55 -
Rwork0.231 1265 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -17.835 Å / Origin y: -36.744 Å / Origin z: -5.995 Å
111213212223313233
T-0.0227 Å2-0.0031 Å20.0264 Å2--0.0818 Å20.0157 Å2---0.1926 Å2
L0.5622 °20.2605 °2-0.0332 °2-2.6013 °20.0891 °2--1.0305 °2
S-0.0035 Å °0.0256 Å °0.1641 Å °-0.1753 Å °0.0276 Å °0.0708 Å °-0.2573 Å °0.0334 Å °-0.0241 Å °

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