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- PDB-4f0z: Crystal Structure of Calcineurin in Complex with the Calcineurin-... -

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Basic information

Entry
Database: PDB / ID: 4f0z
TitleCrystal Structure of Calcineurin in Complex with the Calcineurin-Inhibiting Domain of the African Swine Fever Virus Protein A238L
Components
  • Ankyrin repeat domain-containing protein A238L
  • Calcineurin subunit B type 1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
Keywordshydrolase/protein binding / EF-hand / phosphatase / PxIxIT / LxVP / calcium signaling / transcription regulation / T-cell activation / Calcineurin inhibition / calmodulin / RCAN / NFAT / heart / nucleus / skeletal muscle / ion channels / hydrolase-protein binding complex
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 / protein serine/threonine phosphatase inhibitor activity / negative regulation of dendrite morphogenesis ...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 / protein serine/threonine phosphatase inhibitor activity / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / skeletal muscle tissue regeneration / transition between fast and slow fiber / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / extrinsic component of plasma membrane / dendrite morphogenesis / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine phosphatase activity / branching involved in blood vessel morphogenesis / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / positive regulation of activated T cell proliferation / calcineurin-mediated signaling / positive regulation of endocytosis / Calcineurin activates NFAT / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / multicellular organismal response to stress / phosphatase binding / negative regulation of insulin secretion / skeletal muscle fiber development / keratinocyte differentiation / protein dephosphorylation / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of cell adhesion / hippocampal mossy fiber to CA3 synapse / T cell activation / excitatory postsynaptic potential / wound healing / modulation of chemical synaptic transmission / cellular response to glucose stimulus / sarcolemma / Schaffer collateral - CA1 synapse / Z disc / G1/S transition of mitotic cell cycle / response to calcium ion / protein import into nucleus / calcium ion transport / heart development / ATPase binding / Ca2+ pathway / symbiont-mediated suppression of host NF-kappaB cascade / dendritic spine / host cell cytoplasm / postsynapse / calmodulin binding / 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 / protein-containing complex binding / host cell nucleus / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / plasma membrane / 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 / Ankyrin repeat / EF-hand domain pair / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / 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
IkB-like protein / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
African swine fever virus Malawi LIL 20/1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGrigoriu, S. / Peti, W. / Page, R.
CitationJournal: Plos Biol. / Year: 2013
Title: The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin.
Authors: Grigoriu, S. / Bond, R. / Cossio, P. / Chen, J.A. / Ly, N. / Hummer, G. / Page, R. / Cyert, M.S. / Peti, W.
History
DepositionMay 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_seq_id / _struct_conn.ptnr2_label_asym_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 alpha isoform
B: Calcineurin subunit B type 1
C: Ankyrin repeat domain-containing protein A238L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,18415
Polymers67,2873
Non-polymers89712
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-108 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.691, 48.976, 82.442
Angle α, β, γ (deg.)90.00, 104.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 42855.047 Da / Num. of mol.: 1 / Fragment: Calcineurin A Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q08209, 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: Calcineurin B Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P63098, protein-serine/threonine phosphatase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Ankyrin repeat domain-containing protein A238L / p28


Mass: 5109.087 Da / Num. of mol.: 1 / Fragment: A238L CID (unp residues 200-239)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus Malawi LIL 20/1
Strain: Malawi (Lil 20-1)
Gene: 5EL, Mal-047, Ordered Locus Name: Mal-047 ORF Name: 5EL
Plasmid: pET-RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O36972

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Non-polymers , 3 types, 482 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 470 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.16 M ammonium citrate dibasic, 20% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2011 / Details: Si-111 double crystal monochromator
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 62191 / Num. obs: 60590 / % possible obs: 97.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.73 Å / % possible all: 87.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7.2_869)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AUI

1aui


Resolution: 1.7→47.313 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 2983 5 %
Rwork0.1573 --
obs0.1583 59661 95.83 %
all-62257 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.893 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.577 Å2-0 Å21.1909 Å2
2--1.6565 Å20 Å2
3----1.0795 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 52 470 4904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084619
X-RAY DIFFRACTIONf_angle_d1.0166292
X-RAY DIFFRACTIONf_dihedral_angle_d13.871737
X-RAY DIFFRACTIONf_chiral_restr0.062669
X-RAY DIFFRACTIONf_plane_restr0.005805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.72730.29691180.26982246X-RAY DIFFRACTION80
1.7273-1.75710.34651330.27732492X-RAY DIFFRACTION89
1.7571-1.78910.27281340.28422598X-RAY DIFFRACTION93
1.7891-1.82350.27311360.26352578X-RAY DIFFRACTION92
1.8235-1.86070.28291410.24152641X-RAY DIFFRACTION95
1.8607-1.90120.26461360.21492629X-RAY DIFFRACTION94
1.9012-1.94540.20211430.1942684X-RAY DIFFRACTION95
1.9454-1.9940.22511400.16252706X-RAY DIFFRACTION97
1.994-2.04790.17531420.14642696X-RAY DIFFRACTION96
2.0479-2.10820.191420.13882702X-RAY DIFFRACTION97
2.1082-2.17630.15981440.13442728X-RAY DIFFRACTION97
2.1763-2.2540.14931430.1312727X-RAY DIFFRACTION97
2.254-2.34430.1641450.12932758X-RAY DIFFRACTION98
2.3443-2.4510.14641460.12772772X-RAY DIFFRACTION98
2.451-2.58020.15871450.12872741X-RAY DIFFRACTION98
2.5802-2.74180.16081460.13132782X-RAY DIFFRACTION99
2.7418-2.95350.15631450.12892761X-RAY DIFFRACTION99
2.9535-3.25060.16251500.13292829X-RAY DIFFRACTION99
3.2506-3.72090.14731480.13822825X-RAY DIFFRACTION100
3.7209-4.68720.12091500.1372847X-RAY DIFFRACTION100
4.6872-47.33180.23121560.20732936X-RAY DIFFRACTION100
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)
10.1869-0.05020.09280.169-0.03340.3385-0.02190.06940.0876-0.1785-0.01260.0639-0.2320.01370.02250.11330.0207-0.02170.08170.00140.103527.568345.832562.5747
20.5329-0.1899-0.0920.33640.13990.40650.01690.04850.047-0.0378-0.00180.06630.0249-0.00220.00130.0772-0.0004-0.00690.05720.0070.084630.625624.386956.6521
30.22020.09190.0970.3546-0.13240.19950.01510.0114-0.0856-0.05470.029-0.03770.16690.12760.00890.11710.0408-0.00250.0874-0.020.091345.41268.775556.0528
40.0594-0.01040.02920.34710.23280.17320.01020.01770.01610.0360.0496-0.08030.06230.09020.00170.08790.0086-0.01630.1051-0.01460.092941.189332.924773.8394
50.1357-0.2245-0.01930.93640.08410.00810.0245-0.0925-0.07220.11380.00170.43460.1898-0.1612-0.00610.2282-0.06160.0270.38230.03750.216826.433446.5691118.2887
60.2108-0.2150.05880.52880.05110.05680.1936-0.1077-0.0740.0478-0.20250.0521-0.12270.2367-0.0060.181-0.0399-0.00880.30340.00680.117135.061750.1513107.726
70.3754-0.22340.090.35450.23470.39610.0285-0.0275-0.0390.04570.02690.0236-0.03370.00530.11830.07320.00820.010.0985-0.0130.093228.278445.498188.4905
80.058-0.07980.04690.1105-0.06510.03820.04940.00960.270.07950.0938-0.13580.07240.21030.00240.1693-0.04120.03940.2319-0.06070.170353.716530.388855.2571
90.30980.2854-0.25090.3212-0.11160.4531-0.1668-0.02-0.2579-0.03730.1572-0.110.2170.2425-0.0560.22770.0952-0.04530.2744-0.06730.175545.055634.127786.4808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14:55 ) and not element H
2X-RAY DIFFRACTION2chain 'A' and (resid 56:221 ) and not element H
3X-RAY DIFFRACTION3chain 'A' and (resid 222:304 ) and not element H
4X-RAY DIFFRACTION4chain 'A' and (resid 305:370 ) and not element H
5X-RAY DIFFRACTION5chain 'B' and (resid 6:31 ) and not element H
6X-RAY DIFFRACTION6chain 'B' and (resid 32:81 ) and not element H
7X-RAY DIFFRACTION7chain 'B' and (resid 82:160 ) and not element H
8X-RAY DIFFRACTION8chain 'C' and (resid 205:219 ) and not element H
9X-RAY DIFFRACTION9chain 'C' and (resid 220:234 ) and not element H

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