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- PDB-2f2p: Structure of calmodulin bound to a calcineurin peptide: a new way... -

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Basic information

Entry
Database: PDB / ID: 2f2p
TitleStructure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode
ComponentsCalmodulin fused with calmodulin-binding domain of calcineurin
KeywordsMETAL BINDING PROTEIN / EF-hands / calcium / calmodulin / calcineurin
Function / homology
Function and homology information


CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of signaling / positive regulation of saliva secretion / calcineurin complex / renal filtration / calcineurin-NFAT signaling cascade ...CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of signaling / positive regulation of saliva secretion / calcineurin complex / renal filtration / calcineurin-NFAT signaling cascade / positive regulation of osteoclast differentiation / Ca2+ pathway / dephosphorylation / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of activated T cell proliferation / calcineurin-mediated signaling / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / epidermis development / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of osteoblast differentiation / skeletal muscle fiber development / keratinocyte differentiation / protein dephosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / spindle microtubule / modulation of chemical synaptic transmission / sarcolemma / Z disc / response to calcium ion / spindle pole / myelin sheath / dendritic spine / transmembrane transporter binding / calmodulin binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / metal ion binding / cytosol / 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 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYe, Q. / Wong, A. / Jia, Z.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of calmodulin bound to a calcineurin Peptide: a new way of making an old binding mode.
Authors: Ye, Q. / Li, X. / Wong, A. / Wei, Q. / Jia, Z.
History
DepositionNov 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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_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 fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,17110
Polymers39,8512
Non-polymers3218
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-126 kcal/mol
Surface area17820 Å2
MethodPISA
2
A: Calmodulin fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules

A: Calmodulin fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34220
Polymers79,7014
Non-polymers64116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area12310 Å2
ΔGint-272 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.549, 139.549, 45.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Calmodulin fused with calmodulin-binding domain of calcineurin


Mass: 19925.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P62157, UniProt: Q309F2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→119.523 Å / Num. obs: 15901 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1CDM

1cdm


Resolution: 2.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1495 -random
Rwork0.234 ---
all0.24 ---
obs0.24 14784 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 8 32 2702

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