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- PDB-1cm1: MOTIONS OF CALMODULIN-SINGLE-CONFORMER REFINEMENT -

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Basic information

Entry
Database: PDB / ID: 1cm1
TitleMOTIONS OF CALMODULIN-SINGLE-CONFORMER REFINEMENT
Components
  • CALMODULIN
  • CALMODULIN-DEPENDENT PROTEIN KINASE II-ALPHA
KeywordsCOMPLEX (CALCIUM-BINDING/TRANSFERASE) / COMPLEX (CALCIUM-BINDING-TRANSFERASE) / EF-HAND CALCIUM-BINDING PROTEIN / COMPLEX (CALCIUM-BINDING-TRANSFERASE) complex
Function / homology
Function and homology information


: / peptidyl-threonine autophosphorylation / HSF1-dependent transactivation / neurotransmitter receptor transport to plasma membrane / RAF activation / : / Ion transport by P-type ATPases / DAPK1-calmodulin complex / regulation of mitochondrial membrane permeability involved in apoptotic process / : ...: / peptidyl-threonine autophosphorylation / HSF1-dependent transactivation / neurotransmitter receptor transport to plasma membrane / RAF activation / : / Ion transport by P-type ATPases / DAPK1-calmodulin complex / regulation of mitochondrial membrane permeability involved in apoptotic process / : / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / regulation of store-operated calcium channel activity / dendritic spine development / Interferon gamma signaling / regulation of response to tumor cell / positive regulation of autophagic cell death / Ca2+/calmodulin-dependent protein kinase / : / : / : / : / : / regulation of neuron migration / regulation of neurotransmitter secretion / dendrite morphogenesis / Trafficking of AMPA receptors / : / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / establishment of protein localization to membrane / calcium/calmodulin-dependent protein kinase activity / Ca2+ pathway / RAF/MAP kinase cascade / GTPase activating protein binding / positive regulation of DNA binding / Ion homeostasis / negative regulation of hydrolase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / regulation of synaptic vesicle exocytosis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / calcineurin-mediated signaling / negative regulation of ferroptosis / nitric-oxide synthase binding / regulation of neuronal synaptic plasticity / adenylate cyclase binding / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / regulation of calcium-mediated signaling / catalytic complex / Unblocking of NMDA receptors, glutamate binding and activation / regulation of synaptic vesicle endocytosis / glutamate receptor binding / detection of calcium ion / positive regulation of cardiac muscle cell apoptotic process / response to ischemia / postsynaptic cytosol / regulation of cardiac muscle contraction / cellular response to interferon-beta / regulation of protein localization to plasma membrane / activation of adenylate cyclase activity / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / positive regulation of nitric-oxide synthase activity / presynaptic cytosol / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of heart rate / titin binding / response to amphetamine / voltage-gated potassium channel complex / calcium channel complex / potassium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / positive regulation of receptor signaling pathway via JAK-STAT / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / angiotensin-activated signaling pathway / regulation of cytokinesis / calcium-mediated signaling / spindle microtubule / sarcomere / calcium channel regulator activity / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / myelin sheath / cellular response to type II interferon / response to calcium ion / peptidyl-serine phosphorylation / Schaffer collateral - CA1 synapse / calcium ion transport / spindle pole / disordered domain specific binding
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. / 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 / 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 (domestic 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: Version format compliance
Revision 1.3Aug 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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)19,8087
Polymers19,6082
Non-polymers2005
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-80 kcal/mol
Surface area8570 Å2
MethodPISA
2
A: CALMODULIN
B: CALMODULIN-DEPENDENT PROTEIN KINASE II-ALPHA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)39,61714
Polymers39,2164
Non-polymers40110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
Buried area6490 Å2
ΔGint-177 kcal/mol
Surface area16670 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-600-

CA

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Description: SIGMA LOT 54H9558 / 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: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P11275, EC: 2.7.1.123
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / 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 ENTRIES 1CDM AND 1CDL

1cdm

1cdl


Resolution: 2→10 Å / Rfactor Rfree error: 0.009 / 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
Rfree0.302 1189 10.3 %RANDOM
Rwork0.234 ---
obs0.234 11522 92.1 %-
Displacement parametersBiso mean: 41.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 5 58 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.221.5
X-RAY DIFFRACTIONx_mcangle_it3.882
X-RAY DIFFRACTIONx_scbond_it3.312
X-RAY DIFFRACTIONx_scangle_it5.472.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 128 11.7 %
Rwork0.344 964 -
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_deg21.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72

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