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- PDB-2lhi: Solution structure of Ca2+/CNA1 peptide-bound yCaM -

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Basic information

Entry
Database: PDB / ID: 2lhi
TitleSolution structure of Ca2+/CNA1 peptide-bound yCaM
ComponentsCalmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1
KeywordsMETAL BINDING PROTEIN / yeast calmodulin / CNA1
Function / homology
Function and homology information


regulation of membrane tubulation / cell budding / spindle pole body organization / myosin I complex / cellular response to pheromone / central plaque of spindle pole body / conjugation with cellular fusion / positive regulation of Arp2/3 complex-mediated actin nucleation / karyogamy involved in conjugation with cellular fusion / myosin V complex ...regulation of membrane tubulation / cell budding / spindle pole body organization / myosin I complex / cellular response to pheromone / central plaque of spindle pole body / conjugation with cellular fusion / 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 / calmodulin-dependent protein phosphatase activity / calcineurin complex / vesicle transport along actin filament / microautophagy / vacuole fusion, non-autophagic / fungal-type cell wall organization / incipient cellular bud site / actin cortical patch / cellular bud tip / intracellular monoatomic ion homeostasis / cell tip / cellular bud neck / phosphatidylinositol biosynthetic process / mating projection tip / cellular hyperosmotic response / regulation of cell morphogenesis / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / calcineurin-mediated signaling / enzyme regulator activity / cytoskeleton organization / receptor-mediated endocytosis / microtubule cytoskeleton organization / endocytosis / protein import into nucleus / calcium-dependent protein binding / calmodulin binding / calcium ion binding / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / EF-hand / : ...PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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
Calmodulin / Serine/threonine-protein phosphatase 2B catalytic subunit A1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsOgura, K. / Takahashi, K. / Kobashigawa, Y. / Yoshida, R. / Itoh, H. / Yazawa, M. / Inagaki, F.
CitationJournal: Genes Cells / Year: 2012
Title: Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin.
Authors: Ogura, K. / Kumeta, H. / Takahasi, K. / Kobashigawa, Y. / Yoshida, R. / Itoh, H. / Yazawa, M. / Inagaki, F.
History
DepositionAug 10, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_nmr_software.name / _struct.pdbx_descriptor
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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.status_code_nmr_data / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4024
Polymers19,2821
Non-polymers1203
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1 / CaM / Calcineurin A1 / Calmodulin-binding protein 1


Mass: 19281.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF CALMODULIN (RESIDUE 1-146), LINKER (GSSTG) AND CALCINEURIN A1 (RESIDUES 453-476)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CMD1, YBR109C, YBR0904, CMP1, CNA1, L9753.6, YLR433C / Production host: Escherichia coli (E. coli) / References: UniProt: P06787, UniProt: P23287
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CO)CA
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D C(CO)NH
11113D (H)CCH-TOCSY aliphatic
11213D CCH-TOCSY
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D 1H-15N NOESY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11813D (H)CCH-TOCSY aromatic

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] yCaM_GS_CNA1-1, 20 mM MES-2, 150 mM sodium chloride-3, 5 mM CaCl2-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMyCaM_GS_CNA1-1[U-99% 13C; U-99% 15N]1
20 mMMES-21
150 mMsodium chloride-31
5 mMCaCl2-41
Sample conditionsIonic strength: 150 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe5.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS2003.027.13.05Cornilescu, Delaglio and Baxstructure solution
RNMRTKv3Mobli M, Maciejewski MW, Gryk MR, Hoch JC.processing
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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