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- PDB-1cff: NMR SOLUTION STRUCTURE OF A COMPLEX OF CALMODULIN WITH A BINDING ... -

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Basic information

Entry
Database: PDB / ID: 1cff
TitleNMR SOLUTION STRUCTURE OF A COMPLEX OF CALMODULIN WITH A BINDING PEPTIDE OF THE CA2+-PUMP
Components
  • CALCIUM PUMP
  • CALMODULIN
KeywordsCALMODULIN / C20W / PLASMA MEMBRANE CALCIUM PUMP
Function / homology
Function and homology information


negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / nitric-oxide synthase inhibitor activity / negative regulation of peptidyl-cysteine S-nitrosylation / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / negative regulation of nitric-oxide synthase activity ...negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / nitric-oxide synthase inhibitor activity / negative regulation of peptidyl-cysteine S-nitrosylation / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / negative regulation of nitric-oxide synthase activity / sperm principal piece / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / calcium ion export / response to hydrostatic pressure / flagellated sperm motility / regulation of sodium ion transmembrane transport / urinary bladder smooth muscle contraction / P-type Ca2+ transporter / neural retina development / P-type calcium transporter activity / regulation of cell cycle G1/S phase transition / negative regulation of nitric oxide biosynthetic process / protein phosphatase 2B binding / positive regulation of cAMP-dependent protein kinase activity / calcium ion transmembrane import into cytosol / negative regulation of cardiac muscle hypertrophy in response to stress / Reduction of cytosolic Ca++ levels / negative regulation of calcineurin-NFAT signaling cascade / nitric-oxide synthase binding / negative regulation of blood vessel endothelial cell migration / calcium ion import across plasma membrane / Ion transport by P-type ATPases / transport across blood-brain barrier / regulation of cardiac conduction / sodium channel regulator activity / sperm flagellum / presynaptic active zone membrane / Ion homeostasis / cellular response to epinephrine stimulus / T-tubule / regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / negative regulation of angiogenesis / PDZ domain binding / caveola / hippocampus development / calcium ion transmembrane transport / positive regulation of protein localization to plasma membrane / intracellular calcium ion homeostasis / Z disc / positive regulation of peptidyl-serine phosphorylation / scaffold protein binding / spermatogenesis / basolateral plasma membrane / calmodulin binding / membrane raft / negative regulation of gene expression / signaling receptor binding / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / regulation of transcription by RNA polymerase II / protein kinase binding / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase ...Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / EF-hand / Recoverin; domain 1 / HAD superfamily / HAD-like superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Plasma membrane calcium-transporting ATPase 4 / Calmodulin-2 B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsElshorst, B. / Hennig, M. / Foersterling, H. / Diener, A. / Maurer, M. / Schulte, P. / Schwalbe, H. / Krebs, J. / Schmid, H. / Vorherr, T. ...Elshorst, B. / Hennig, M. / Foersterling, H. / Diener, A. / Maurer, M. / Schulte, P. / Schwalbe, H. / Krebs, J. / Schmid, H. / Vorherr, T. / Carafoli, E. / Griesinger, C.
CitationJournal: Biochemistry / Year: 1999
Title: NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+ pump.
Authors: Elshorst, B. / Hennig, M. / Forsterling, H. / Diener, A. / Maurer, M. / Schulte, P. / Schwalbe, H. / Griesinger, C. / Krebs, J. / Schmid, H. / Vorherr, T. / Carafoli, E.
History
DepositionMar 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Aug 29, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: CALMODULIN
B: CALCIUM PUMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3846
Polymers19,2232
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 200LOWEST ENERGY
Representative

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Components

#1: Protein CALMODULIN / / CAM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Strain: 71 / Cellular location (production host): CYTOPLASM / Gene (production host): CALMODULIN / Production host: Escherichia coli (E. coli) / Strain (production host): AR58 / References: UniProt: P62155, UniProt: P0DP33*PLUS
#2: Protein/peptide CALCIUM PUMP /


Mass: 2501.997 Da / Num. of mol.: 1 / Fragment: CAM-BINDING DOMAIN / Mutation: C20W / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P23634, EC: 3.6.1.38
#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
111HNCO
121HNCA
131CBCA(CO)NH
141CBCANH
151(H)CC(CO)NH
161(H)CCH-TOCSY
171NOESY-HSQC
NMR detailsText: THE UNLABELED PEPTIDE C20W WAS ASSIGNED USING A 12C,14N-FILTERED NOESY- EXPERIMENT. INTERMOLECULAR NOES BETWEEN 13C,15N-LABELED CALMODULIN AND THE PEPTIDE WERE MEASURED USING A 12C,14N-F2- ...Text: THE UNLABELED PEPTIDE C20W WAS ASSIGNED USING A 12C,14N-FILTERED NOESY- EXPERIMENT. INTERMOLECULAR NOES BETWEEN 13C,15N-LABELED CALMODULIN AND THE PEPTIDE WERE MEASURED USING A 12C,14N-F2-FILTERED NOESY-HSQC EXPERIMENT

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Sample preparation

DetailsContents: 90% H2O/10% D2O, 100% D2O
Sample conditionsIonic strength: 0.115 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX600BrukerDRX6006001
Bruker DRX800BrukerDRX8008002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
XPLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IT IS IMPOSSIBLE TO SUPERIMPOSE THE N- AND C-TERMINAL DOMAIN OF CAM SIMULTANEOUSLY DUE TO THE LACK OF NOES BETWEEN BOTH DOMAINS. ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IT IS IMPOSSIBLE TO SUPERIMPOSE THE N- AND C-TERMINAL DOMAIN OF CAM SIMULTANEOUSLY DUE TO THE LACK OF NOES BETWEEN BOTH DOMAINS. THEREFOR THE 26 STRUCTURES ARE SUPERIMPOSED ONLY OVER THE BACKBONE ATOMS OF THE C-TERMINAL DOMAIN OF CAM AND THE PEPTIDE C20W. RMSD VALUES OF THE N-TERMINAL DOMAIN OF CAM (LEU A 4 - ALA A 73) ARE 0.85 (BACKBONE) AND 1.27 (HEAVY ATOMS) ANGSTROMS. RMSD VALUE FOR THE C- TERMINAL DOMAIN OF CAM AND THE PEPTIDE C20W (ILE A 85 - MET A 145, GLY B 4 - GLN B 16) ARE 0.57 (BACKBONE) AND 1.08 (HEAVY ATOMS) ANGSTROMS. RESIDUES ALA A 1 - GLN A 3, ARG A 74 - GLU A 84, THR A 146 - LYS A 148 OF CAM AND RESIDUES LEU B 1 - ARG B 3, THR B 17 - LYS B 20 OF THE PEPTIDE C20W ARE DISORDERED.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 26

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