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- PDB-1sy9: Structure of calmodulin complexed with a fragment of the olfactor... -

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Basic information

Entry
Database: PDB / ID: 1sy9
TitleStructure of calmodulin complexed with a fragment of the olfactory CNG channel
Components
  • CALMODULIN
  • Cyclic-nucleotide-gated olfactory channel
KeywordsCALCIUM-BINDING PROTEIN / 4 helix-turn-helix
Function / homology
Function and homology information


non-motile cilium membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / myosin II complex / sodium ion transport / monoatomic cation transmembrane transport / monoatomic ion channel activity / cGMP binding / cAMP binding ...non-motile cilium membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / myosin II complex / sodium ion transport / monoatomic cation transmembrane transport / monoatomic ion channel activity / cGMP binding / cAMP binding / potassium ion transport / calcium channel activity / calcium ion transport / sensory perception of smell / calmodulin binding / signaling receptor binding / calcium ion binding / protein-containing complex binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / EF-hand / : / Recoverin; domain 1 / RmlC-like jelly roll fold / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 B / Cyclic nucleotide-gated channel alpha-2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsContessa, G.M. / Orsale, M. / Melino, S. / Torre, V. / Paci, M. / Desideri, A. / Cicero, D.O.
Citation
Journal: J.Biomol.Nmr / Year: 2005
Title: Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.
Authors: Contessa, G.M. / Orsale, M. / Melino, S. / Torre, V. / Paci, M. / Desideri, A. / Cicero, D.O.
#1: Journal: FEBS Lett. / Year: 2003
Title: Two distinct Ca2+-Calmodulin interactions with N-terminal regions of the olfactory and rod cyclic nucleotide gated channels characterized by NMR spectroscopy
Authors: Orsale, M. / Melino, S. / Contessa, G.M. / Torre, V. / Andreotti, G. / Motta, A. / Paci, M. / Desideri, A. / Cicero, D.O.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALMODULIN
B: Cyclic-nucleotide-gated olfactory channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1516
Polymers19,9912
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
Representative

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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.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS
#2: Protein/peptide Cyclic-nucleotide-gated olfactory channel / Cyclic-nucleotide-gated cation channel 2 / CNG channel 2 / CNG-2 / CNG2


Mass: 3269.817 Da / Num. of mol.: 1 / Fragment: Residues 151-176 / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence of the protein is naturally found in Bos Taurus (bovine).
References: UniProt: Q03041
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
142HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM complex U-15N,13C, 6 mM CaCl2, 140 mM KCl, D2OD2O
21.2 mM complex U-15N,13C, 6 mM CaCl2, 140 mM KCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHTemperature (K)
16.7308 K
26.7308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
NMRPipedata analysis
X-PLOR3.85refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 3935 restraints: 3050 are NOE-derived distance constraints, 591 are dihedral angle restraints, 133 are distance restraints from hydrogen bonds. 68 ...Details: The structures are based on a total of 3935 restraints: 3050 are NOE-derived distance constraints, 591 are dihedral angle restraints, 133 are distance restraints from hydrogen bonds. 68 scalar J coupling constants and 93 Residual Dipolar Coupling constants were included as experimental restraints necessary to obtain the final structures.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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