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- PDB-5c1v: CRYSTAL STRUCTURE ANALYSIS OF CATALYTIC SUBUNIT OF HUMAN CALCINEURIN -

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Basic information

Entry
Database: PDB / ID: 5c1v
TitleCRYSTAL STRUCTURE ANALYSIS OF CATALYTIC SUBUNIT OF HUMAN CALCINEURIN
ComponentsSerine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHYDROLASE / 4-LAYER SANDWICH / SERINE/THREONINE PHOSPHATASE / CALCIUM BINDING
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 / 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 ...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 / 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 / calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / renal filtration / positive regulation of calcineurin-NFAT signaling cascade / transition between fast and slow fiber / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / dendrite morphogenesis / cyclosporin A binding / myosin phosphatase activity / 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 / negative regulation of insulin secretion / epidermis development / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / dephosphorylation / keratinocyte differentiation / response to amphetamine / excitatory postsynaptic potential / 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 / ATPase binding / dendritic spine / protein dimerization activity / calmodulin binding / positive regulation of cell migration / 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
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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsGuasch, A. / Fita, I. / Perez-Luque, R. / Aparicio, D. / Aranguren-Ibanez, A. / Perez-Riba, M.
Funding support Spain, 4items
OrganizationGrant numberCountry
Ministerio Ciencia InnovacionBFU2012-36827 Spain
Generalitat de Catalunya2014SGR927 Spain
Ministerio Ciencia InnovacionSAF2009-08216 Spain
Generalitat de Catalunya2009SGR1490 Spain
CitationJournal: Plos One / Year: 2015
Title: Calcineurin Undergoes a Conformational Switch Evoked via Peptidyl-Prolyl Isomerization.
Authors: Guasch, A. / Aranguren-Ibanez, A. / Perez-Luque, R. / Aparicio, D. / Martinez-Hyer, S. / Mulero, M.C. / Serrano-Candelas, E. / Perez-Riba, M. / Fita, I.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _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

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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: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9798
Polymers79,5472
Non-polymers4326
Water0
1
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9904
Polymers39,7731
Non-polymers2163
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9904
Polymers39,7731
Non-polymers2163
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.008, 185.008, 106.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 24 - 340 / Label seq-ID: 23 - 339

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.571673, -0.332942, -0.749893), (-0.077586, -0.887935, 0.453378), (-0.816805, 0.317365, 0.481777)-26.35279, -142.42581, 19.02346

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Components

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


Mass: 39773.363 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 2-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 25% PEG 3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 111
SYNCHROTRONSLS X06DA21
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELJul 2, 2012
DECTRIS PILATUS 2M2PIXELMay 24, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTALSINGLE WAVELENGTHMx-ray1
2MICRO DIFFRACTOMETER MKII (MD2)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 3.35→47.8 Å / Num. obs: 15994 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 13
Reflection shellResolution: 3.35→3.53 Å / Rmerge(I) obs: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUI

1aui


Resolution: 3.35→47.8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 65.827 / SU ML: 0.446 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 823 5.1 %RANDOM
Rwork0.216 ---
obs0.217 15172 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.22 Å2
Baniso -1Baniso -2Baniso -3
1--5.55 Å2-5.55 Å2-0 Å2
2---5.55 Å2-0 Å2
3---18 Å2
Refinement stepCycle: LAST / Resolution: 3.35→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5063 0 14 0 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195190
X-RAY DIFFRACTIONr_bond_other_d0.0060.024856
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9617030
X-RAY DIFFRACTIONr_angle_other_deg1.293311167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4655624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02723.735257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.34615864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91532
X-RAY DIFFRACTIONr_chiral_restr0.110.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215874
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021256
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_it3.8224.5792505
X-RAY DIFFRACTIONr_mcbond_other3.8224.582504
X-RAY DIFFRACTIONr_mcangle_it6.0886.8693126
X-RAY DIFFRACTIONr_mcangle_other5.3268.3313127
X-RAY DIFFRACTIONr_scbond_it3.8094.8842683
X-RAY DIFFRACTIONr_scbond_other3.4085.8872670
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9098.7233887
X-RAY DIFFRACTIONr_long_range_B_refined10.00947.4988716
X-RAY DIFFRACTIONr_long_range_B_other10.00947.4968717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18275 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 78 -
Rwork0.364 1065 -
obs--100 %
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)
14.43181.57420.97374.9390.83283.4201-0.0107-0.14640.40920.1056-0.0782-0.0254-0.1620.31180.0890.0560.0626-0.02160.57150.05750.3703-27.5641-68.98725.7133
211.02672.4656-1.97254.29750.22872.6972-0.0584-1.2793-0.12550.98180.0528-0.88950.3747-0.18740.00560.73280.1193-0.12731.2311-0.12250.22747.3323-65.938728.4278
30.3646-1.0361-0.77872.98762.23381.6996-0.1594-0.0117-0.23980.382-0.13950.47290.44620.00510.29891.4394-0.07330.03391.77480.30281.7035-0.794-90.115132.4698
414.7453-13.2204-1.864911.86371.67320.24570.66360.56641.83-0.6576-0.5013-1.5397-0.0278-0.0721-0.16220.85170.1568-0.17741.5097-0.04781.562910.8409-78.093712.4154
50.02910.1720.04693.31640.43260.08770.1098-0.02070.09490.513-0.2221-0.26480.1353-0.05340.11231.0991-0.02570.06271.29810.09980.7986-15.2202-81.75431.1127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 340
2X-RAY DIFFRACTION2B23 - 235
3X-RAY DIFFRACTION2B262 - 282
4X-RAY DIFFRACTION2B298 - 325
5X-RAY DIFFRACTION3B236 - 261
6X-RAY DIFFRACTION4B326 - 340
7X-RAY DIFFRACTION5B290 - 297

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