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- PDB-1cdm: MODULATION OF CALMODULIN PLASTICITY IN MOLECULAR RECOGNITION ON T... -

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Basic information

Entry
Database: PDB / ID: 1cdm
TitleMODULATION OF CALMODULIN PLASTICITY IN MOLECULAR RECOGNITION ON THE BASIS OF X-RAY STRUCTURES
Components
  • CALMODULIN
  • PEPTIDE CALMODULIN-DEPENDENT PROTEIN KINASE II
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


HSF1-dependent transactivation / regulation of synaptic vesicle docking / glutamatergic postsynaptic density / RAF activation / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / calmodulin dependent kinase signaling pathway / Interferon gamma signaling ...HSF1-dependent transactivation / regulation of synaptic vesicle docking / glutamatergic postsynaptic density / RAF activation / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / calmodulin dependent kinase signaling pathway / Interferon gamma signaling / calcium-dependent protein serine/threonine kinase activity / NMDA selective glutamate receptor signaling pathway / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / Trafficking of AMPA receptors / Ca2+ pathway / positive regulation of calcium ion transport / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / presynaptic cytosol / negative regulation of hydrolase activity / calmodulin-dependent protein kinase activity / RAF/MAP kinase cascade / GTPase activating protein binding / dendrite morphogenesis / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / regulation of neuronal synaptic plasticity / Ion homeostasis / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle cell apoptotic process / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / cellular response to interferon-beta / regulation of protein localization to plasma membrane / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / response to ischemia / angiotensin-activated signaling pathway / G1/S transition of mitotic cell cycle / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / spindle pole / cellular response to type II interferon / calcium ion transport / kinase activity / dendritic spine / postsynaptic density / calmodulin binding / neuron projection / axon / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
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. / EF-hand calcium-binding domain profile. ...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
Calcium/calmodulin-dependent protein kinase type II subunit alpha / Calmodulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMeador, W.E. / Quiocho, F.A.
Citation
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.
#1: Journal: Science / Year: 1992
Title: Target Enzyme Recognition by Calmodulin: 2.4 Angstroms Structure of a Calmodulin-Peptide Complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
History
DepositionOct 8, 1993Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.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.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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,3256
Polymers19,1642
Non-polymers1604
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-77 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.000, 75.200, 120.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PEPTIDE CALMODULIN-DEPENDENT PROTEIN KINASE II


Mass: 16277.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P62157
#2: Protein/peptide CALMODULIN /


Mass: 2886.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P11275
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
Rwork0.208 -
obs0.208 9535
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 4 53 1236
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.28

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