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- PDB-4il1: Crystal Structure of the Rat Calcineurin -

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Basic information

Entry
Database: PDB / ID: 4il1
TitleCrystal Structure of the Rat Calcineurin
ComponentsCalmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHYDROLASE / Calcium-binding protein / chimera protein / fusion protein / Protein phosphatase
Function / homology
Function and homology information


Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / FCERI mediated Ca+2 mobilization / negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / regulation of store-operated calcium channel activity / negative regulation of signaling ...Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / FCERI mediated Ca+2 mobilization / negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / regulation of store-operated calcium channel activity / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / : / regulation of high voltage-gated calcium channel activity / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion-dependent exocytosis / : / establishment of protein localization to mitochondrial membrane / myelination in peripheral nervous system / type 3 metabotropic glutamate receptor binding / transition between fast and slow fiber / Ca2+ pathway / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / establishment of protein localization to membrane / regulation of synaptic vesicle cycle / dendrite morphogenesis / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / 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 / branching involved in blood vessel morphogenesis / 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 postsynaptic neurotransmitter receptor internalization / regulation of cardiac muscle cell action potential / parallel fiber to Purkinje cell synapse / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle hypertrophy / negative regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of activated T cell proliferation / calcineurin-mediated signaling / positive regulation of endocytosis / regulation of synaptic vesicle endocytosis / phosphoprotein phosphatase activity / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / protein localization to nucleus / epidermis development / epithelial to mesenchymal transition / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / multicellular organismal response to stress / phosphatase binding / presynaptic cytosol / negative regulation of insulin secretion / Schwann cell development / calcium channel inhibitor activity / cellular response to interferon-beta / skeletal muscle fiber development / keratinocyte differentiation / protein dephosphorylation / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / EF hand 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 ...PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / EF hand 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
Calmodulin-1 / Calmodulin-1 / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYe, Q. / Faucher, F. / Jia, Z.
CitationJournal: Cell Signal / Year: 2013
Title: Structural basis of calcineurin activation by calmodulin.
Authors: Ye, Q. / Feng, Y. / Yin, Y. / Faucher, F. / Currie, M.A. / Rahman, M.N. / Jin, J. / Li, S. / Wei, Q. / Jia, Z.
History
DepositionDec 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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_ncs_dom_lim / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
C: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
D: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,43620
Polymers370,7954
Non-polymers64116
Water2,234124
1
A: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8595
Polymers92,6991
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8595
Polymers92,6991
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8595
Polymers92,6991
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8595
Polymers92,6991
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.300, 193.850, 107.820
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA163 - 809163 - 809
21BB163 - 809163 - 809
12AA163 - 809163 - 809
22CC163 - 809163 - 809
13AA163 - 809163 - 809
23DD163 - 809163 - 809
14BB163 - 809163 - 809
24CC163 - 809163 - 809
15BB163 - 810163 - 810
25DD163 - 810163 - 810
16CC163 - 809163 - 809
26DD163 - 809163 - 809

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / CaM / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B ...CaM / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1 / CAM-PRP catalytic subunit / Calmodulin-dependent calcineurin A subunit alpha isoform


Mass: 92698.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm, Calm1, Calm2, Calm3, Calna, Cam, Cam1, Cam2, Cam3, Camb, Camc, Ppp3ca, Cn a2, Cnb, Ppp3r1
Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P62161, UniProt: P63100, UniProt: P63329, UniProt: P0DP29*PLUS, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY ...THE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY TWO GLYCINE LINKERS BETWEEN THEM. THE CLONING CONSTRUCT ORDER FOR THESE THREE PROTEINS IS CALMODULIN CAM [FIRST PROTEIN], CALCINEURIN SUBUNIT B CNB [SECOND PROTEIN] AND CALCINEURIN SUBUNIT A CNA [THIRD PROTEIN]. THE FIRST GLYCINE LINKER IS BETWEEN C-TERMINUS OF CAM AND N-TERMINUS OF CNB, AND THE SECOND GLYCINE LINKER IS BETWEEN C-TERMINUS OF CNB AND N-TERMINUS OF CNA. THE CNA WAS TRUNCATED AT ITS C-TERMINUS D483-Q511, AND THEN ADDED WITH AN UNCLEAVED C-TERMINAL HIS-TAG. THE SEQUENCE ORDER IS CAM-9XGLY-CNB-6XGLY-CNA482-LEHHHHHH.

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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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 293 K / pH: 5.6
Details: PEG 3350, 1-Propanol, Citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2009 / Details: SYNCHROTRON OPTICS
RadiationMonochromator: MONOCHROMATIC MACROMOLECULAR CRYSTALLOGRAPHY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 81046 / % possible obs: 99.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.1 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF8

1mf8


Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.535 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.939 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2002 2.5 %RANDOM
Rwork0.241 ---
obs0.242 79044 99.4 %-
all-81046 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.91 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å2-0.18 Å2
2---0.75 Å2-0 Å2
3---4.33 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17115 0 16 124 17255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917416
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216382
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.96123538
X-RAY DIFFRACTIONr_angle_other_deg1.315337692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98752102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32124.276884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.963153005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.40215107
X-RAY DIFFRACTIONr_chiral_restr0.0780.22524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119787
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5016.0288444
X-RAY DIFFRACTIONr_mcbond_other4.5016.0288443
X-RAY DIFFRACTIONr_mcangle_it7.0569.02810534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A314930.13
12B314930.13
21A312810.14
22C312810.14
31A310860.14
32D310860.14
41B312590.13
42C312590.13
51B313450.14
52D313450.14
61C308540.15
62D308540.15
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 138 -
Rwork0.297 5692 -
obs--99.71 %

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