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- PDB-4ora: Crystal structure of a human calcineurin mutant -

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Basic information

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


calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / protein serine/threonine phosphatase complex / locomotion involved in locomotory behavior / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / positive regulation of lysosome organization / calcineurin complex ...calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / protein serine/threonine phosphatase complex / locomotion involved in locomotory behavior / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / positive regulation of lysosome organization / calcineurin complex / negative regulation of T cell mediated cytotoxicity / calcineurin-mediated signaling / ROBO receptors bind AKAP5 / lymphangiogenesis / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / regulation of synaptic vesicle cycle / positive regulation of calcineurin-NFAT signaling cascade / calcium-ion regulated exocytosis / myelination in peripheral nervous system / protein phosphatase 2B binding / axon extension / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / regulation of synaptic vesicle endocytosis / cyclosporin A binding / branching involved in blood vessel morphogenesis / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / postsynaptic modulation of chemical synaptic transmission / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / T cell homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Calcineurin activates NFAT / T cell differentiation / DARPP-32 events / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / phosphatase binding / skeletal muscle fiber development / T cell proliferation / dephosphorylation / T-tubule / T cell activation / hippocampal mossy fiber to CA3 synapse / FCERI mediated Ca+2 mobilization / protein dephosphorylation / learning / response to cytokine / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / T cell mediated cytotoxicity / sarcolemma / memory / Z disc / positive regulation of protein localization to nucleus / protein import into nucleus / Ca2+ pathway / heart development / postsynapse / protein dimerization activity / calmodulin binding / protein domain specific binding / protein phosphorylation / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / 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
: / Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform / Calcineurin subunit B type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.747 Å
AuthorsLi, 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 1.1Nov 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_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 / _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_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 beta isoform
B: Calcineurin subunit B type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8998
Polymers80,6172
Non-polymers2826
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-50 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.203, 108.203, 284.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 61294.504 Da / Num. of mol.: 1 / Mutation: V418Y, F419L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALNA2, CALNB, CNA2, PPP3CB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P16298, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNA2, CNB, PPP3R1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63098

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Non-polymers , 4 types, 51 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 / Iron


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 / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM MES, pH 5.8, 9% PEG 3350, 4% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.91939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91939 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. all: 26604 / Num. obs: 24485 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.3 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 28.4
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2597 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUI

1aui


Resolution: 2.747→46.994 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1246 5.09 %RANDOM
Rwork0.1991 ---
obs0.2016 24485 91.99 %-
all-26604 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7443 Å22.7443 Å2-5.4885 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.747→46.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 6 45 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014675
X-RAY DIFFRACTIONf_angle_d1.2126328
X-RAY DIFFRACTIONf_dihedral_angle_d14.9871759
X-RAY DIFFRACTIONf_chiral_restr0.083679
X-RAY DIFFRACTIONf_plane_restr0.005832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7472-2.85720.3007770.257160558
2.8572-2.98720.29191120.2503218580
2.9872-3.14470.31461420.2581255693
3.1447-3.34160.28061540.2362270598
3.3416-3.59960.2441620.2142274799
3.5996-3.96160.2491560.189275499
3.9616-4.53450.19521390.1487281099
4.5345-5.71140.21781560.16672840100
5.7114-47.00050.25751480.199303799
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)
10.61010.002-0.09470.6123-0.51280.4439-0.07680.20930.118-0.56440.13570.30590.2552-0.1649-0.11690.4002-0.0842-0.11760.16660.02360.2029-25.759828.6813-6.6074
21.2966-0.05220.2310.87050.01161.6132-0.062-0.09410.1011-0.0113-0.0584-0.0121-0.1388-0.0070.02830.0966-0.0431-0.07260.0390.04880.0718-14.732432.7723.8786
30.7498-0.56130.66880.8142-1.02881.3221-0.2446-0.09160.36650.23390.1031-0.2258-0.3106-0.15560.13820.2763-0.0463-0.11740.13510.03430.2277-21.0353.44450.4727
42.2905-0.0676-1.58174.4843-0.4661.55940.1295-1.1754-0.80940.87470.2208-0.21640.80260.2989-0.13550.39470.0596-0.14110.43870.07950.2645-17.875558.7688-0.8799
50.1913-0.24310.39970.3495-0.49830.8376-0.12960.00710.43250.08470.0048-0.2325-0.53150.2880.18760.8002-0.056-0.18220.4174-0.0441.042-12.34650.757721.8276
61.2354-1.08390.6041.2896-0.4871.1753-0.0445-0.04090.23710.10820.0112-0.1527-0.1059-0.11530.00460.1733-0.0214-0.06450.15370.10090.2119-33.070960.555-14.5491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:51)A15 - 51
2X-RAY DIFFRACTION2chain 'A' and (resseq 52:334)A52 - 334
3X-RAY DIFFRACTION3chain 'A' and (resseq 335:386)A335 - 386
4X-RAY DIFFRACTION4chain 'A' and (resseq 416:422)A416 - 422
5X-RAY DIFFRACTION5chain 'A' and (resseq 478:495)A478 - 495
6X-RAY DIFFRACTION6chain 'B' and (resseq 4:169)B4 - 169

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