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- PDB-2p6b: Crystal Structure of Human Calcineurin in Complex with PVIVIT Peptide -

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Basic information

Entry
Database: PDB / ID: 2p6b
TitleCrystal Structure of Human Calcineurin in Complex with PVIVIT Peptide
Components
  • Calcineurin subunit B isoform 1
  • Calmodulin-dependent calcineurin A subunit alpha isoform
  • PVIVIT 14-mer Peptide
KeywordsHYDROLASE/HYDROLASE REGULATOR / Beta-sheet Augmentation / Protein-peptide Complex / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / slit diaphragm / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / peptidyl-serine dephosphorylation / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / renal filtration / regulation of synaptic vesicle cycle / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / transition between fast and slow fiber / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / dendrite morphogenesis / parallel fiber to Purkinje cell synapse / cyclosporin A binding / myosin phosphatase activity / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / extrinsic component of plasma membrane / postsynaptic modulation of chemical synaptic transmission / positive regulation of endocytosis / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / Calcineurin activates NFAT / DARPP-32 events / positive regulation of cell adhesion / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / negative regulation of insulin secretion / epidermis development / phosphatase binding / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / dephosphorylation / keratinocyte differentiation / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / T cell activation / FCERI mediated Ca+2 mobilization / protein dephosphorylation / cellular response to glucose stimulus / G1/S transition of mitotic cell cycle / sarcolemma / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / wound healing / Z disc / response to calcium ion / protein import into nucleus / calcium ion transport / Ca2+ pathway / heart development / ATPase binding / postsynapse / dendritic spine / protein dimerization activity / calmodulin binding / positive regulation of cell migration / protein domain specific binding / negative regulation of gene expression / glutamatergic synapse / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calcineurin B protein / 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 ...Calcineurin B protein / 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
: / PHOSPHATE ION / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, H. / Zhang, L. / Rao, A. / Harrison, S.C. / Hogan, P.G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structure of calcineurin in complex with PVIVIT peptide: Portrait of a low-affinity signalling interaction
Authors: Li, H. / Zhang, L. / Rao, A. / Harrison, S.C. / Hogan, P.G.
#1: Journal: 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.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: X-ray Structure of Calcineurin Inhibited by the Immunophilin-immunosuppressant FKBP12-FK506 Complex
Authors: Griffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A.
#3: Journal: Science / Year: 1999
Title: Affinity-driven Peptide Selection of an NFAT Inhibitor More Selective Than Cyclosporin A
Authors: Aramburu, J. / Yaffe, M.B. / Lopez-Rodriguez, C. / Cantley, L.C. / Hogan, P.G. / Rao, A.
#4: Journal: J.Mol.Biol. / Year: 2004
Title: Structural Delineation of the Calcineurin-NFAT Interaction and Its Parallels to PP1 Targeting Interactions
Authors: Li, H. / Rao, A. / Hogan, P.G.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
E: PVIVIT 14-mer Peptide
A: Calmodulin-dependent calcineurin A subunit alpha isoform
B: Calcineurin subunit B isoform 1
C: Calmodulin-dependent calcineurin A subunit alpha isoform
D: Calcineurin subunit B isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,72719
Polymers124,9745
Non-polymers75314
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.104, 89.155, 157.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAlthough the asymmetric unit contains two calcineurin AB heterodimers, the functional unit in solution is a single AB heterodimer

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Components

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Protein/peptide , 1 types, 1 molecules E

#1: Protein/peptide PVIVIT 14-mer Peptide


Mass: 1481.673 Da / Num. of mol.: 1 / Fragment: Residues 3-16 / Source method: obtained synthetically / Details: Synthetic Peptide

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Protein , 2 types, 4 molecules ACBD

#2: Protein Calmodulin-dependent calcineurin A subunit alpha isoform / E.C.3.1.3.16 / Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / CAM-PRP catalytic subunit


Mass: 43991.188 Da / Num. of mol.: 2 / Fragment: Residues 1-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08209
#3: Protein Calcineurin subunit B isoform 1 / / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 17755.174 Da / Num. of mol.: 2 / Fragment: Residues 16-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63098

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Non-polymers , 5 types, 578 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 4000, 0.1M calcium chloride, 0.1M TES, 0.001M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2006
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60710 / % possible obs: 96.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.104 / Χ2: 1.563 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.529 / Num. unique all: 4593 / Χ2: 1.279 / % possible all: 73.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å42.9 Å
Translation2.5 Å42.9 Å

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AUI

1aui


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5173 9.5 %Random
Rwork0.192 ---
obs-51123 93.5 %-
Solvent computationBsol: 36.056 Å2
Displacement parametersBiso mean: 37.883 Å2
Baniso -1Baniso -2Baniso -3
1-2.985 Å20 Å20 Å2
2---1.679 Å20 Å2
3----1.306 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8283 0 22 564 8869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it1.5551.5
X-RAY DIFFRACTIONc_scbond_it2.2282
X-RAY DIFFRACTIONc_mcangle_it2.6162
X-RAY DIFFRACTIONc_scangle_it3.3872.5
LS refinement shellHighest resolution: 2.3 Å
RfactorNum. reflection
Rfree0.2543 5173
Rwork0.1924 -
obs-51123
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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