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- PDB-4orc: Crystal structure of mammalian calcineurin -

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Basic information

Entry
Database: PDB / ID: 4orc
TitleCrystal structure of mammalian calcineurin
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 / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / locomotion involved in locomotory behavior / calmodulin-dependent protein phosphatase activity / calcineurin complex / negative regulation of T cell mediated cytotoxicity / positive regulation of calcium ion import across plasma membrane / positive regulation of lysosome organization ...calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / locomotion involved in locomotory behavior / calmodulin-dependent protein phosphatase activity / calcineurin complex / negative regulation of T cell mediated cytotoxicity / positive regulation of calcium ion import across plasma membrane / positive regulation of lysosome organization / ROBO receptors bind AKAP5 / lymphangiogenesis / protein serine/threonine phosphatase complex / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / calcium-ion regulated exocytosis / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / protein phosphatase 2B binding / regulation of synaptic vesicle cycle / axon extension / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / response to stress / parallel fiber to Purkinje cell synapse / calcineurin-mediated signaling / protein serine/threonine phosphatase activity / T cell homeostasis / T cell differentiation / Calcineurin activates NFAT / epithelial to mesenchymal transition / DARPP-32 events / Activation of BAD and translocation to mitochondria / regulation of synaptic vesicle endocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phosphatase binding / postsynaptic modulation of chemical synaptic transmission / T cell proliferation / protein dephosphorylation / skeletal muscle fiber development / response to cytokine / T-tubule / FCERI mediated Ca+2 mobilization / regulation of insulin secretion / T cell activation / hippocampal mossy fiber to CA3 synapse / learning / sarcolemma / T cell mediated cytotoxicity / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Schaffer collateral - CA1 synapse / memory / Z disc / protein import into nucleus / heart development / Ca2+ pathway / calmodulin binding / protein phosphorylation / postsynapse / protein dimerization activity / protein domain specific binding / calcium ion binding / positive regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol
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
: / PHOSPHATE ION / 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: 2.7 Å
AuthorsMa, L. / Li, 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 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 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)80,9649
Polymers80,5872
Non-polymers3777
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-161 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.200, 110.200, 282.488
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: 61264.473 Da / Num. of mol.: 1 / Fragment: catalytic subunit
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 / Fragment: regulatory subunit
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 , 5 types, 48 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 100mM MES, pH 6.1, 10% PEG3350, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28850 / Num. obs: 28655 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.7 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3 / Num. unique all: 1410 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUI

1aui


Resolution: 2.7→39.538 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1453 5.07 %RANDOM
Rwork0.2153 ---
obs0.2176 28655 99.55 %-
all-28850 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 6.932 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-38.5145 Å2-0 Å20 Å2
2--38.5145 Å2-0 Å2
3---0.1925 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 11 41 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094491
X-RAY DIFFRACTIONf_angle_d1.2056081
X-RAY DIFFRACTIONf_dihedral_angle_d16.6441676
X-RAY DIFFRACTIONf_chiral_restr0.085655
X-RAY DIFFRACTIONf_plane_restr0.005798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.79650.35911390.3128261498
2.7965-2.90840.34081580.30082646100
2.9084-3.04080.32421540.2832652100
3.0408-3.2010.28631230.27042698100
3.201-3.40150.34631560.2819262898
3.4015-3.66390.26461510.23022709100
3.6639-4.03230.25341500.20752702100
4.0323-4.6150.21891300.16092770100
4.615-5.81150.23511420.18192799100
5.8115-39.54270.19161500.17642984100
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)
10.1509-0.15230.03380.54940.42320.5389-0.02510.1544-0.0156-0.21910.072-0.2263-0.09210.1478-0.06860.308-0.08360.11870.2061-0.0340.203227.2785-29.0845-7.6464
20.6055-0.0059-0.10490.4189-0.10911.0884-0.00290.0297-0.026-0.0724-0.0891-0.04040.06230.09470.02740.0752-0.01640.07060.062-0.02620.068420.0835-29.80418.2565
32.2169-0.1850.05830.76580.15511.42820.0393-0.3018-0.29230.0872-0.15870.02290.27740.07180.09510.1857-0.04110.03610.14470.02350.144115.2678-38.776236.3137
40.6464-0.15660.28450.70950.01680.988-0.0005-0.082-0.12780.0186-0.09060.14750.203-0.20210.10730.1181-0.05570.04490.0872-0.08190.10764.9824-37.330529.4003
51.1475-1.0102-0.75711.07370.74790.5306-0.2416-0.0609-0.3640.13410.04740.23250.20720.04190.1540.2815-0.00790.08730.2475-0.06020.242822.0116-54.23090.3737
62.1362-0.2717-1.02191.43130.06726.87450.01650.0916-0.0927-0.1819-0.053-0.00970.0901-0.08530.0080.11950.0204-0.05190.2377-0.08370.290849.3034-70.7409-23.9625
70.47550.7015-0.27361.28470.02070.87830.0488-0.1546-0.40950.0485-0.05630.12590.3414-0.0377-0.01690.23960.01950.05140.2359-0.04370.409742.0732-79.0294-18.2716
80.169-0.20940.16261.05320.64051.0498-0.00790.0393-0.41510.0333-0.09590.37660.1368-0.23040.21050.1528-0.0130.03150.2596-0.15090.481528.19-70.3775-19.7356
91.5-0.22870.12051.5928-0.3091.4203-0.0701-0.0920.0162-0.0165-0.07860.16760.0319-0.07210.10590.15970.0270.03760.2479-0.05660.21840.4535-66.536-19.3096
100.6423-0.5522-0.16651.0042-0.0580.26670.01930.0309-0.00440.01160.0622-0.12930.09280.1606-0.00810.2512-0.00770.07060.2554-0.14230.242238.9715-56.3146-10.8042
110.6575-0.4002-0.44470.77150.41321.3175-0.0113-0.04920.00910.11710.0805-0.0768-0.0060.02470.22830.1989-0.02820.07730.2166-0.14070.231825.9026-47.0621-10.5413
120.1967-0.04790.0791.73151.03180.77580.0444-0.09530.05010.17220.0359-0.0829-0.00230.1716-0.03770.2522-0.01420.00450.4299-0.21080.286738.9187-49.0541-5.2293
131.94340.46280.51141.0843-0.15881.9935-0.1316-0.31380.14030.3719-0.01680.04590.0415-0.08810.0650.4640.12920.06130.44-0.00790.297740.07-65.6719-3.2612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 13:51)A13 - 51
2X-RAY DIFFRACTION2chain 'A' and (resseq 52:218)A52 - 218
3X-RAY DIFFRACTION3chain 'A' and (resseq 219:256)A219 - 256
4X-RAY DIFFRACTION4chain 'A' and (resseq 257:334)A257 - 334
5X-RAY DIFFRACTION5chain 'A' and (resseq 335:421)A335 - 421
6X-RAY DIFFRACTION6chain 'B' and (resseq 4:15)B4 - 15
7X-RAY DIFFRACTION7chain 'B' and (resseq 16:29)B16 - 29
8X-RAY DIFFRACTION8chain 'B' and (resseq 30:61)B30 - 61
9X-RAY DIFFRACTION9chain 'B' and (resseq 62:86)B62 - 86
10X-RAY DIFFRACTION10chain 'B' and (resseq 87:98)B87 - 98
11X-RAY DIFFRACTION11chain 'B' and (resseq 99:148)B99 - 148
12X-RAY DIFFRACTION12chain 'B' and (resseq 149:159)B149 - 159
13X-RAY DIFFRACTION13chain 'B' and (resseq 160:169)B160 - 169

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