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- PDB-4fg7: Crystal structure of human calcium/calmodulin-dependent protein k... -

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Basic information

Entry
Database: PDB / ID: 4fg7
TitleCrystal structure of human calcium/calmodulin-dependent protein kinase I 1-293 in complex with ATP
ComponentsCalcium/calmodulin-dependent protein kinase type 1
KeywordsTRANSFERASE / CaMK / calmodulin / autoinhibition / regulation mechanism / kinase
Function / homology
Function and homology information


positive regulation of syncytium formation by plasma membrane fusion / regulation of protein binding / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / nucleocytoplasmic transport / positive regulation of muscle cell differentiation / Activation of RAC1 downstream of NMDARs / regulation of synapse organization ...positive regulation of syncytium formation by plasma membrane fusion / regulation of protein binding / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / nucleocytoplasmic transport / positive regulation of muscle cell differentiation / Activation of RAC1 downstream of NMDARs / regulation of synapse organization / positive regulation of dendritic spine development / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of protein serine/threonine kinase activity / negative regulation of protein binding / positive regulation of protein export from nucleus / positive regulation of neuron projection development / nervous system development / regulation of protein localization / cell differentiation / calmodulin binding / protein phosphorylation / postsynaptic density / intracellular signal transduction / protein serine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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. ...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
ADENOSINE-5'-TRIPHOSPHATE / Calcium/calmodulin-dependent protein kinase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZha, M. / Zhong, C. / Ou, Y. / Wang, J. / Han, L. / Ding, J.
CitationJournal: Plos One / Year: 2012
Title: Crystal structures of human CaMKIalpha reveal insights into the regulation mechanism of CaMKI.
Authors: Zha, M. / Zhong, C. / Ou, Y. / Han, L. / Wang, J. / Ding, J.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7112
Polymers33,2041
Non-polymers5071
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.681, 65.681, 139.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1 / CaM kinase I / CaM-KI / CaM kinase I alpha / CaMKI-alpha


Mass: 33203.660 Da / Num. of mol.: 1 / Fragment: residues 1-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14012, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200mM NH4Ac, 100mM (CH3)2AsO2Na, 25% PEG 8000, pH 6.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→59.46 Å / Num. all: 8967 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 33.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A06

1a06


Resolution: 2.7→59.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 461 5.2 %RANDOM
Rwork0.2201 ---
obs0.2214 8918 99.25 %-
all-8967 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.41 Å2 / Biso mean: 51.0192 Å2 / Biso min: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→59.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 31 79 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222087
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9862832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1195246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56924.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.64158
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0930.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211570
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)1.231.51244
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)2.19322000
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)2.9953843
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)4.5944.5832
X-RAY DIFFRACTIONRIGID-BOND RESTRAINTS (A''2)1.68232087
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 27 -
Rwork0.241 609 -
all-636 -
obs--97.7 %
Refinement TLS params.Method: refined / Origin x: 129.3778 Å / Origin y: -22.3634 Å / Origin z: 24.2949 Å
111213212223313233
T0.1232 Å2-0.0037 Å2-0.0124 Å2-0.169 Å20.0326 Å2--0.0438 Å2
L1.0607 °2-0.834 °2-0.2944 °2-2.7372 °2-0.2469 °2--0.3986 °2
S0.0294 Å °0.058 Å °0.1097 Å °0.1406 Å °-0.0171 Å °-0.035 Å °0.0706 Å °0.0583 Å °-0.0122 Å °

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