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- PDB-1aui: HUMAN CALCINEURIN HETERODIMER -

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Basic information

Entry
Database: PDB / ID: 1aui
TitleHUMAN CALCINEURIN HETERODIMER
Components(SERINE/THREONINE PHOSPHATASE ...) x 2
KeywordsHYDROLASE / PHOSPHATASE / IMMUNOSUPPRESSION
Function / homology
Function and homology information


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 / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / peptidyl-serine dephosphorylation / calmodulin-dependent protein phosphatase activity ...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 / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / peptidyl-serine dephosphorylation / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of calcium ion import across plasma membrane / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / positive regulation of connective tissue replacement / positive regulation of cardiac muscle hypertrophy in response to stress / negative regulation of dendrite morphogenesis / protein serine/threonine phosphatase complex / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / positive regulation of calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / transition between fast and slow fiber / myelination in peripheral nervous system / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / dephosphorylation / extrinsic component of plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / dendrite morphogenesis / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / calcineurin-mediated signaling / protein serine/threonine phosphatase activity / positive regulation of activated T cell proliferation / Calcineurin activates NFAT / epithelial to mesenchymal transition / DARPP-32 events / positive regulation of endocytosis / epidermis development / Activation of BAD and translocation to mitochondria / positive regulation of osteoblast differentiation / phosphatase binding / multicellular organismal response to stress / postsynaptic modulation of chemical synaptic transmission / protein dephosphorylation / keratinocyte differentiation / skeletal muscle fiber development / FCERI mediated Ca+2 mobilization / positive regulation of cell adhesion / T cell activation / hippocampal mossy fiber to CA3 synapse / excitatory postsynaptic potential / wound healing / G1/S transition of mitotic cell cycle / response to calcium ion / sarcolemma / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / Z disc / protein import into nucleus / calcium ion transport / heart development / ATPase binding / Ca2+ pathway / 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 / positive regulation of gene expression / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / plasma membrane / 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 / 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
: / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR PLUS ANOMALOUS SCATTERING / Resolution: 2.1 Å
AuthorsKissinger, C.R. / Parge, H.E. / Knighton, D.R. / Pelletier, L.A. / Lewis, C.T. / Tempczyk, A. / Villafranca, J.E.
CitationJournal: Nature / Year: 1995
Title: Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex.
Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / ...Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / Chen, X. / Maldonado, F. / Barker, J.E. / Bacquet, R. / Villafranca, J.E.
History
DepositionAug 27, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Feb 7, 2024Group: 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_struct_conn_angle / software / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _software.name / _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_conn.ptnr2_label_seq_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: SERINE/THREONINE PHOSPHATASE 2B
B: SERINE/THREONINE PHOSPHATASE 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2308
Polymers77,9482
Non-polymers2826
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-139 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.810, 104.340, 177.770
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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SERINE/THREONINE PHOSPHATASE ... , 2 types, 2 molecules AB

#1: Protein SERINE/THREONINE PHOSPHATASE 2B / CALCINEURIN


Mass: 58756.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#2: Protein SERINE/THREONINE PHOSPHATASE 2B / CALCINEURIN


Mass: 19191.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P63098, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 442 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.: 436 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 6000, 0.1M CACL2, 0.1M TES PH 7.5, 1 MM DTT.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDChemical formula
1PEG600011
211CaCl2

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Data collection

DiffractionMean temperature: 87 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 50007 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.069
Reflection
*PLUS
Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
HASSPmodel building
HEAVYmodel building
MLPHAREphasing
PHASESphasing
XTALVIEWrefinement
X-PLOR3.1refinement
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
HASSPphasing
HEAVYphasing
RefinementMethod to determine structure: MIR PLUS ANOMALOUS SCATTERING
Resolution: 2.1→10 Å / Isotropic thermal model: UNRESTRAINED
Details: SIDE CHAIN ATOMS WITHOUT DISCERNIBLE ELECTRON DENSITY HAVE BEEN MODELLED IN STEREOCHEMICALLY REASONABLE POSITIONS AND ASSIGNED OCCUPANCIES OF ZERO.
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 48504 90.8 %
Displacement parametersBiso mean: 39.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 6 436 4832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.94

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