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- PDB-2r28: The complex Structure of Calmodulin Bound to a Calcineurin Peptide -

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Basic information

Entry
Database: PDB / ID: 2r28
TitleThe complex Structure of Calmodulin Bound to a Calcineurin Peptide
Components
  • Calmodulin
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsMETAL BINDING PROTEIN/Hydrolase / Protein-peptide complex / Acetylation / Calcium / Methylation / Phosphorylation / Ubl conjugation / Alternative splicing / Calmodulin-binding / Hydrolase / Iron / Metal-binding / Nucleus / Protein phosphatase / Zinc / METAL BINDING PROTEIN-Hydrolase COMPLEX
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / renal filtration / calcineurin-NFAT signaling cascade / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / skeletal muscle tissue regeneration / transition between fast and slow fiber / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / extrinsic component of plasma membrane / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / dendrite morphogenesis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / protein serine/threonine phosphatase activity / mitochondrion-endoplasmic reticulum membrane tethering / histone H2AXS139 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 / autophagosome membrane docking / myosin phosphatase activity / regulation of synaptic vesicle exocytosis / protein-serine/threonine phosphatase / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of activated T cell proliferation / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / positive regulation of endocytosis / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Calcineurin activates NFAT / protein phosphatase activator activity / Regulation of MECP2 expression and activity / regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase binding / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / epidermis development / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission
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 domain pair ...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 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
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYe, Q. / Zheng, J. / Jia, Z.
CitationJournal: Proteins / Year: 2008
Title: The complex structure of calmodulin bound to a calcineurin peptide.
Authors: Ye, Q. / Wang, H. / Zheng, J. / Wei, Q. / Jia, Z.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
C: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calmodulin
D: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,63712
Polymers39,3164
Non-polymers3218
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-41 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.7, 43.2, 70.9
Angle α, β, γ (deg.)90, 109.9, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1092-

HOH

21B-1107-

HOH

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Components

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 2 / Fragment: Calmodulin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiens / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / Calmodulin-dependent calcineurin A subunit alpha isoform / CAM-PRP catalytic subunit


Mass: 2805.458 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Bos taurus / Gene: PPP3CA, CALNA, CNA / Plasmid: pET21a_CciT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 0.2M ammonium phosphate, 0.1M citrite acid , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9124 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.85→66.67 Å / Num. all: 29453 / Num. obs: 28898 / % possible obs: 98.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.06 / Net I/σ(I): 9
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 8.1 / Num. unique all: 2632 / Rsym value: 0.873 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F2O

2f2o


Resolution: 1.86→66.67 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.28 5 Random
Rwork0.23 --
obs0.23 26242 -
all-27976 -
Refinement stepCycle: LAST / Resolution: 1.86→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 8 258 2803
LS refinement shellResolution: 1.86→1.91 Å / Rfactor Rfree error: 0.17
RfactorNum. reflection
Rfree0.28 1397
Rwork0.23 -
obs-26242

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