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- PDB-1cm4: Motions of calmodulin-four-conformer refinement -

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Basic information

Entry
Database: PDB / ID: 1cm4
TitleMotions of calmodulin-four-conformer refinement
Components
  • CALMODULIN
  • CALMODULIN-DEPENDENT PROTEIN KINASE II-ALPHA
KeywordsCALCIUM-BINDING/TRANSFERASE / EF-HAND CALCIUM-BINDING PROTEIN / CALCIUM-BINDING-TRANSFERASE complex
Function / homology
Function and homology information


regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / regulation of high voltage-gated calcium channel activity / neurotransmitter receptor transport to plasma membrane ...regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / regulation of store-operated calcium channel activity / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / regulation of high voltage-gated calcium channel activity / neurotransmitter receptor transport to plasma membrane / : / calcium- and calmodulin-dependent protein kinase complex / Interferon gamma signaling / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / regulation of neuron migration / dendritic spine development / calcium-dependent protein serine/threonine kinase activity / : / establishment of protein localization to mitochondrial membrane / Trafficking of AMPA receptors / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / Ca2+ pathway / negative regulation of hydrolase activity / establishment of protein localization to membrane / postsynaptic neurotransmitter receptor diffusion trapping / presynaptic cytosol / GTPase activating protein binding / RAF/MAP kinase cascade / dendrite morphogenesis / postsynaptic specialization membrane / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of synaptic vesicle endocytosis / calcium/calmodulin-dependent protein kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Ion homeostasis / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle cell apoptotic process / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / regulation of neuronal synaptic plasticity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / Unblocking of NMDA receptors, glutamate binding and activation / regulation of protein localization to plasma membrane / calcium channel inhibitor activity / glutamate receptor binding / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / response to ischemia / angiotensin-activated signaling pathway / spindle microtubule / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / cellular response to type II interferon / G2/M transition of mitotic cell cycle / spindle pole
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / NTF2-like domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / : / NTF2-like domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calcium/calmodulin-dependent protein kinase type II subunit alpha / Calmodulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWall, M.E. / Phillips Jr., G.N.
Citation
Journal: Structure / Year: 1997
Title: Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering.
Authors: Wall, M.E. / Clarage, J.B. / Phillips Jr., G.N.
#1: Journal: Science / Year: 1993
Title: Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
#2: Journal: Science / Year: 1992
Title: Target Enzyme Recognition by Calmodulin: 2.4 A Structure of a Calmodulin-Peptide Complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
History
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2013Group: Structure summary
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
B: CALMODULIN-DEPENDENT PROTEIN KINASE II-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,28919
Polymers19,6082
Non-polymers68117
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-27 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.751, 75.209, 120.073
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-417-

CA

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA LOT 54H9558 / Source: (natural) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P02593, UniProt: P62157*PLUS
#2: Protein/peptide CALMODULIN-DEPENDENT PROTEIN KINASE II-ALPHA


Mass: 2886.528 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING DOMAIN, RESIDUES 290 - 314 / Source method: obtained synthetically / References: UniProt: P11275, EC: 2.7.1.123
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growMethod: vapor diffusion - hanging drop - microseeding / pH: 5.2
Details: DIFFRACTION-QUALITY CRYSTALS WERE MICROSEEDED IN HANGING DROPS OVER 100 MM SODIUM ACETATE AT PH 5.2, WITH 20% POLY-ETHYLENE GLYCOL 6000 (PEG 6000), 10 MM CALCIUM CHLORIDE AND 0.02% SODIUM ...Details: DIFFRACTION-QUALITY CRYSTALS WERE MICROSEEDED IN HANGING DROPS OVER 100 MM SODIUM ACETATE AT PH 5.2, WITH 20% POLY-ETHYLENE GLYCOL 6000 (PEG 6000), 10 MM CALCIUM CHLORIDE AND 0.02% SODIUM AZIDE. STOCK SOLUTIONS OF 24 MG/ML BOVINE BRAIN CALMODULIN (SIGMA LOT 54H9558), 14 MG/ML CAMKII-ALPHA PEPTIDE, AND 30% PEG WERE MIXED INTO HANGING DROPS IN ABOUT A 4-2-1 RATIO., vapor diffusion - hanging drop - microseeding
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium acetate1reservoir
220 %PEG60001reservoir
310 mM1reservoirCaCl2
40.02 %sodium azide1reservoir
514 mg/mlbovine1drop
64 mg/mlpeptide1drop
74.3 %PEG60001drop

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Data collection

DiffractionMean temperature: 302 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98
DetectorType: PRINCETON 2K / Detector: CCD / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: SINGLE-CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 11522 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.24 / % possible all: 82.8

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CM1

1cm1


Resolution: 2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES 74 - 83, WHICH ARE NOT PRESENT IN PDB ENTRY 1CDM, WERE ADDED FOR THIS REFINEMENT. AN INITIAL GUESS WAS OBTAINED FROM THE COORDINATES OF PDB ENTRY 1CDL. THESE RESIDUES DO NOT SHOW ...Details: RESIDUES 74 - 83, WHICH ARE NOT PRESENT IN PDB ENTRY 1CDM, WERE ADDED FOR THIS REFINEMENT. AN INITIAL GUESS WAS OBTAINED FROM THE COORDINATES OF PDB ENTRY 1CDL. THESE RESIDUES DO NOT SHOW CONNECTED ELECTRON DENSITY AT A LEVEL OF 1SIGMA.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1189 10.3 %RANDOM
Rwork0.166 ---
obs0.166 11522 92.1 %-
Displacement parametersBiso mean: 29.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 17 58 1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.362
X-RAY DIFFRACTIONx_scbond_it1.952
X-RAY DIFFRACTIONx_scangle_it2.932.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.261 128 11.7 %
Rwork0.233 964 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78

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