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- PDB-4orb: Crystal structure of mouse calcineurin -

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Basic information

Entry
Database: PDB / ID: 4orb
TitleCrystal structure of mouse calcineurin
Components
  • Calcineurin subunit B type 1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHYDROLASE/METAL BINDING PROTEIN / Calmodulin-binding / HYDROLASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


Activation of BAD and translocation to mitochondria / 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 / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / Calcineurin activates NFAT ...Activation of BAD and translocation to mitochondria / 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 / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / Calcineurin activates NFAT / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of calcium ion import across plasma membrane / positive regulation of connective tissue replacement / Ca2+ pathway / positive regulation of cardiac muscle hypertrophy in response to stress / negative regulation of dendrite morphogenesis / FCERI mediated Ca+2 mobilization / protein serine/threonine phosphatase complex / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / transition between fast and slow fiber / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / branching involved in blood vessel morphogenesis / dendrite morphogenesis / protein-serine/threonine phosphatase / positive regulation of cardiac muscle hypertrophy / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / positive regulation of activated T cell proliferation / phosphoprotein phosphatase activity / positive regulation of endocytosis / epithelial to mesenchymal transition / protein localization to nucleus / epidermis development / positive regulation of osteoblast differentiation / phosphatase binding / postsynaptic modulation of chemical synaptic transmission / multicellular organismal response to stress / Schwann cell development / protein dephosphorylation / keratinocyte differentiation / skeletal muscle fiber development / hippocampal mossy fiber to CA3 synapse / excitatory postsynaptic potential / calcium-mediated signaling / G1/S transition of mitotic cell cycle / sarcolemma / response to calcium ion / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cytoplasmic side of plasma membrane / Z disc / protein import into nucleus / calcium ion transport / heart development / ATPase binding / dendritic spine / calmodulin binding / postsynapse / protein dimerization activity / positive regulation of cell migration / protein domain specific binding / negative regulation of gene expression / calcium ion binding / synapse / positive regulation of gene expression / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / 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 / 4-Layer Sandwich / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Protein phosphatase 3 catalytic subunit alpha / Calcineurin subunit B type 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.108 Å
AuthorsMa, L. / Li, S.J. / Wang, J. / Wu, J.W. / Wang, Z.X.
CitationJournal: To be Published
Title: Cooperative autoinhibition and multi-level activation mechanisms of calcineurin
Authors: Li, S.J. / Ma, L. / Wang, J. / Lu, C. / Wang, J. / Wu, J.W. / Wang, Z.X.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 8, 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.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_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_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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcineurin subunit B type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3598
Polymers78,0782
Non-polymers2826
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-47 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.865, 107.466, 175.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / CAM-PRP catalytic subunit / Calmodulin-dependent calcineurin A subunit alpha isoform


Mass: 58754.734 Da / Num. of mol.: 1 / Fragment: catalytic subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calna, Ppp3ca / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63328, protein-serine/threonine phosphatase
#2: Protein Calcineurin subunit B type 1 / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 19322.904 Da / Num. of mol.: 1 / Fragment: regulatory subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnb, Ppp3r1 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63810

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Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAMINO ACIDS (447-456) ARE MISSING BECAUSE THIS SEQUENCE CORRESPONDS TO THE ISOFORM2 FOUND IN UNP P63328.

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 100mM MES, pH 6.1, 18% PEG3350, 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 17090 / Num. obs: 17038 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.273 / Num. unique all: 1587 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUI

1aui


Resolution: 3.108→39.691 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 868 5.09 %RANDOM
Rwork0.1959 ---
obs0.1982 17038 97.92 %-
all-17090 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.512 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.249 Å20 Å2-0 Å2
2--23.8704 Å20 Å2
3----0.5449 Å2
Refinement stepCycle: LAST / Resolution: 3.108→39.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 6 15 4399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014478
X-RAY DIFFRACTIONf_angle_d1.2766049
X-RAY DIFFRACTIONf_dihedral_angle_d15.4081676
X-RAY DIFFRACTIONf_chiral_restr0.082651
X-RAY DIFFRACTIONf_plane_restr0.005791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.108-3.30250.31011370.2839250293
3.3025-3.55740.26321510.2176256695
3.5574-3.91510.25341350.191267999
3.9151-4.48090.20521610.15612737100
4.4809-5.64290.22931420.17962763100
5.6429-39.69390.25461420.20682923100
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)
13.0724-0.37390.71471.5959-0.53081.3247-0.02040.39740.1358-0.1620.00860.0147-0.03670.20460.02130.231-0.04030.0080.29490.03960.207810.1519-22.7875-19.1483
21.9469-0.59751.24131.5199-0.20990.72610.4635-0.1722-0.0835-0.4256-0.4947-0.69180.5970.64530.19120.67950.1427-0.0650.81780.17930.576610.2033-15.6855-50.9102
30.6098-0.12820.6441.7516-3.41423.84320.1111-0.1478-0.1878-0.3826-0.0183-0.10830.4677-0.0067-0.04780.64390.0181-0.03950.4590.04020.4264-5.7633-4.7858-61.5959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 14:348)A14 - 348
2X-RAY DIFFRACTION2chain 'A' and (resseq 349:475)A349 - 475
3X-RAY DIFFRACTION3chain 'B' and (resseq 5:169)B5 - 169

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