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- PDB-4q5u: Structure of calmodulin bound to its recognition site from calcineurin -

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Basic information

Entry
Database: PDB / ID: 4q5u
TitleStructure of calmodulin bound to its recognition site from calcineurin
Components
  • Calmodulin
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsCALCIUM BINDING PROTEIN/PROTEIN BINDING / EF hand / CALCIUM BINDING PROTEIN-PROTEIN BINDING 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 / autophagosome membrane docking / 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 / regulation of synaptic vesicle exocytosis / myosin phosphatase activity / 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 / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of activated T cell proliferation / 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 / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / 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: 1.95 Å
AuthorsGuo, H. / Dunlap, T.B. / Creamer, T.P. / Vander Kooi, C.W.
CitationJournal: Biochemistry / Year: 2014
Title: Stoichiometry of the calcineurin regulatory domain-calmodulin complex.
Authors: Dunlap, T.B. / Guo, H.F. / Cook, E.C. / Holbrook, E. / Rumi-Masante, J. / Lester, T.E. / Colbert, C.L. / Vander Kooi, C.W. / Creamer, T.P.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 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_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_asym_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_asym_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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8336
Polymers19,6732
Non-polymers1604
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-74 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.499, 111.033, 39.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

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Components

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pETCaMI / 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 / CAM-PRP catalytic subunit / Calmodulin-dependent calcineurin A subunit alpha isoform


Mass: 2820.496 Da / Num. of mol.: 1 / Fragment: calmodulin-binding domain (UNP residues 391-414) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q08209
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3:1 10 mg/ml protein to mother liquor (24% PEG1000, 20% glycerol), final volume 200 nL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→19.12 Å / Num. obs: 15779 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.4 / % possible all: 69.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W73

2w73


Resolution: 1.95→19.12 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 801 5.08 %RANDOM
Rwork0.2147 ---
obs0.2165 15779 90.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 4 100 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061352
X-RAY DIFFRACTIONf_angle_d0.9721810
X-RAY DIFFRACTIONf_dihedral_angle_d14.43524
X-RAY DIFFRACTIONf_chiral_restr0.07200
X-RAY DIFFRACTIONf_plane_restr0.004244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.07160.3421000.27111902X-RAY DIFFRACTION70
2.0716-2.23130.29661110.24722211X-RAY DIFFRACTION82
2.2313-2.45550.26081450.23642531X-RAY DIFFRACTION93
2.4555-2.80980.27241420.23142714X-RAY DIFFRACTION100
2.8098-3.53640.22951510.22812749X-RAY DIFFRACTION100
3.5364-19.12110.23541520.19142871X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8011-0.6887-2.58268.36052.72684.4845-0.1732-0.0153-0.2597-0.1124-0.05150.0840.40120.05830.31390.45810.0503-0.05650.4150.02590.440732.773610.21436.8774
25.6530.0406-0.28182.76-0.31999.32380.2090.2182-0.20680.0644-0.36180.10890.9835-0.3170.19750.50420.0595-0.11190.4474-0.01140.506931.215322.8885-4.3999
34.47940.1059-0.35384.9089-3.92523.343-0.0861-0.14670.59880.2157-0.8049-1.376-0.40581.7490.73220.3862-0.0185-0.09140.77420.10010.920645.258228.1702-1.9114
49.989-2.274-1.8637.8131.08187.19950.0810.4257-0.0722-0.3109-0.2869-0.13530.28940.00880.07760.46680.016-0.10250.42210.02150.426934.831917.7501-0.2849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:73)
2X-RAY DIFFRACTION2(chain A and resid 74:97)
3X-RAY DIFFRACTION3(chain A and resid 98:147)
4X-RAY DIFFRACTION4(chain C and resid 391:414)

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