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- PDB-1f54: SOLUTION STRUCTURE OF THE APO N-TERMINAL DOMAIN OF YEAST CALMODULIN -

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Basic information

Entry
Database: PDB / ID: 1f54
TitleSOLUTION STRUCTURE OF THE APO N-TERMINAL DOMAIN OF YEAST CALMODULIN
ComponentsCALMODULIN
KeywordsTRANSPORT PROTEIN / EF-hand / helix-loop-helix
Function / homology
Function and homology information


regulation of membrane tubulation / cell budding / spindle pole body organization / myosin I complex / central plaque of spindle pole body / positive regulation of Arp2/3 complex-mediated actin nucleation / karyogamy involved in conjugation with cellular fusion / myosin V complex / regulation of microtubule nucleation / cellular bud ...regulation of membrane tubulation / cell budding / spindle pole body organization / myosin I complex / central plaque of spindle pole body / positive regulation of Arp2/3 complex-mediated actin nucleation / karyogamy involved in conjugation with cellular fusion / myosin V complex / regulation of microtubule nucleation / cellular bud / microautophagy / vesicle transport along actin filament / vacuole fusion, non-autophagic / incipient cellular bud site / actin cortical patch / cellular bud tip / cell tip / cellular bud neck / phosphatidylinositol biosynthetic process / mating projection tip / cellular hyperosmotic response / mitogen-activated protein kinase binding / enzyme regulator activity / cytoskeleton organization / receptor-mediated endocytosis / microtubule cytoskeleton organization / endocytosis / protein import into nucleus / calcium-dependent protein binding / calcium ion binding / cytoplasm
Similarity search - Function
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 ...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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsIshida, H. / Takahashi, K. / Nakashima, K. / Kumaki, Y. / Nakata, M. / Hikichi, K. / Yazawa, M.
CitationJournal: Biochemistry / Year: 2000
Title: Solution Structures of the N-terminal Domain of Yeast Calmodulin: Ca2+-Dependent Conformational Change and Its Functional Implication
Authors: Ishida, H. / Takahashi, K. / Nakashima, K. / Kumaki, Y. / Nakata, M. / Hikichi, K. / Yazawa, M.
History
DepositionJun 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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


Theoretical massNumber of molelcules
Total (without water)8,5461
Polymers8,5461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
Representative

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Components

#1: Protein CALMODULIN


Mass: 8546.367 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: INTRACELLULAR CALCIUM SENSOR
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET-30B(+) AND PIC10 / Production host: Escherichia coli (E. coli) / References: UniProt: P06787

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
1423D 15N-separated NOESY
1523D 15N-separated TOCSY
16215N-HSQC
1732D NOESY
NMR detailsText: The structure was determined using double-resonance NMR spectroscopy on 15N-labeled protein

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM N-terminal domain of Yeast Calmodulin; 50 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
23 mM N-terminal domain of Yeast Calmodulin U-15N; 50 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
33 mM N-terminal domain of Yeast Calmodulin; 50 mM KCl; 99.99% D2O99.99% D2O
Sample conditionsIonic strength: 50 mM KCl / pH: 6.8 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: JEOL A / Manufacturer: JEOL / Model: A / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 996 restraints, 917 are NOE-derived distance constraints, 44 dihedral angle restraints, 35 distance restraints from hydrogen bonds
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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