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- PDB-7u0t: Crystal Structure of a human Calcineurin A - Calcineurin B fusion... -

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Basic information

Entry
Database: PDB / ID: 7u0t
TitleCrystal Structure of a human Calcineurin A - Calcineurin B fusion bound to FKBP12 and FK-520
Components
  • Peptidylprolyl isomerase
  • Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform,Calcineurin subunit B type 1 fusion
KeywordsHYDROLASE/ISOMERASE / SSGCID / CnA / CnB / FKBP12 / peptidyl prolyl cis-trans isomerase / phosphatase / FK-520 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / HYDROLASE-ISOMERASE complex / Anti-fungal
Function / homology
Function and homology information


myosin phosphatase activity / calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade ...myosin phosphatase activity / calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / positive regulation of synaptic vesicle endocytosis / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / regulation of synaptic vesicle cycle / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / calcineurin-mediated signaling / Calcineurin activates NFAT / epithelial to mesenchymal transition / DARPP-32 events / Activation of BAD and translocation to mitochondria / phosphatase binding / postsynaptic modulation of chemical synaptic transmission / protein dephosphorylation / FCERI mediated Ca+2 mobilization / hippocampal mossy fiber to CA3 synapse / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / sarcolemma / Schaffer collateral - CA1 synapse / protein import into nucleus / presynapse / heart development / Ca2+ pathway / calmodulin binding / postsynapse / protein domain specific binding / calcium ion binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / metal ion binding / 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 / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / FKBP-type peptidyl-prolyl cis-trans isomerase ...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 / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / EF-hand / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KXX / Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform / Calcineurin subunit B type 1 / peptidylprolyl isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsFox III, D. / Mayclin, S.J. / DeBouver, N.D. / Hoy, M.J. / Heitman, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2022
Title: Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus.
Authors: Hoy, M.J. / Park, E. / Lee, H. / Lim, W.Y. / Cole, D.C. / DeBouver, N.D. / Bobay, B.G. / Pierce, P.G. / Fox 3rd, D. / Ciofani, M. / Juvvadi, P.R. / Steinbach, W. / Hong, J. / Heitman, J.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform,Calcineurin subunit B type 1 fusion
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7628
Polymers43,7482
Non-polymers1,0146
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.100, 33.300, 64.350
Angle α, β, γ (deg.)90.000, 103.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform,Calcineurin subunit B type 1 fusion / CAM-PRP catalytic subunit / Calcineurin / testis-specific catalytic subunit / Calmodulin-dependent ...CAM-PRP catalytic subunit / Calcineurin / testis-specific catalytic subunit / Calmodulin-dependent calcineurin A subunit gamma isoform / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 27115.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CC, CALNA3, CNA3, PPP3R1, CNA2, CNB / Plasmid: HosaA.00174.a.TU11, HosaA.01011.a.TV11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P48454, UniProt: P63098, protein-serine/threonine phosphatase
#2: Protein Peptidylprolyl isomerase


Mass: 16632.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A / Plasmid: HosaA.18272.a.TM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0VDC6, peptidylprolyl isomerase

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Non-polymers , 4 types, 68 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-KXX / (3S,4R,5S,8R,9E,12S,14S,15R,16S,18R,19R,22R,26aS)-8-ethyl-5,19-dihydroxy-3-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-14,16-dimethoxy-4,10,12,18-tetramethyl-5,6,8,11,12,13,14,15,16,17,18,19,24,25,26,26a-hexadecahydro-3H-15,19-epoxypyrido[2,1-c][1,4]oxazacyclotricosine-1,7,20,21(4H,23H)-tetrone


Mass: 792.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H69NO12 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 49.27 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Microlytics MCSG-1 C5: 0.2M Magnesium Acetate, 20% PEG 3,350, HosaA.18272.a.TM11.PD38439 at 20mg/ml + FK-520 (Purified from SEC): cryo: 20% ethylene glycol: tray 318701c5, puck oxo8-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→31.67 Å / Num. obs: 11961 / % possible obs: 97.8 % / Redundancy: 3.524 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.084 / Χ2: 0.931 / Net I/σ(I): 13.22 / Num. measured all: 42156 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.512.6830.372.647570.8360.45885
2.51-2.582.9280.3792.688360.8270.46392.4
2.58-2.663.4190.3153.788180.8960.37499.4
2.66-2.743.6870.2774.78150.9280.32599.8
2.74-2.833.7490.2225.657860.9610.2699.6
2.83-2.933.7370.1986.527770.9630.232100
2.93-3.043.6980.1528.567520.9760.17999.7
3.04-3.163.7450.1239.756930.9860.14499.9
3.16-3.33.6880.09312.887090.9910.10999.3
3.3-3.463.7180.07715.386550.9920.0999.2
3.46-3.653.6680.066186180.9930.07799.7
3.65-3.873.6450.05919.235830.9940.06999
3.87-4.143.6570.04622.825660.9960.05598.8
4.14-4.473.6340.03926.545190.9970.04699
4.47-4.93.5920.03827.114980.9970.045100
4.9-5.483.5650.0425.464370.9970.04799.1
5.48-6.333.570.04422.883950.9970.05299.7
6.33-7.753.4860.03526.793310.9980.04298.8
7.75-10.963.3150.03132.082700.9980.03798.9
10.96-31.673.0410.02632.851460.9980.03190.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.45 Å31.67 Å
Translation2.45 Å31.67 Å

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Processing

Software
NameVersionClassification
PHENIXv1.20refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCO

1tco


Resolution: 2.45→31.67 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1196 10 %
Rwork0.2111 10762 -
obs0.2161 11958 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.3 Å2 / Biso mean: 50.5788 Å2 / Biso min: 20.14 Å2
Refinement stepCycle: final / Resolution: 2.45→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 64 62 2394
Biso mean--31.54 38.66 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022382
X-RAY DIFFRACTIONf_angle_d0.5123231
X-RAY DIFFRACTIONf_dihedral_angle_d17.215866
X-RAY DIFFRACTIONf_chiral_restr0.041362
X-RAY DIFFRACTIONf_plane_restr0.003424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.550.33841170.28481055117287
2.55-2.660.34681300.26821165129598
2.66-2.80.28161360.255712241360100
2.8-2.980.32891320.258311911323100
2.98-3.210.32091330.249711991332100
3.21-3.530.25631330.21131201133499
3.53-4.040.24371370.19621234137199
4.04-5.080.2191360.16212141350100
5.09-31.670.22311420.1941279142199
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)
12.289-0.7874-0.59657.72344.12843.1364-0.0650.0093-0.0278-0.4831-0.3913-0.4880.6973-0.18910.3780.66790.01930.03810.24750.06810.343931.893712.90053.2071
25.46856.16710.32487.0547-0.23323.3164-0.30420.33870.07880.91980.07330.29250.32780.43130.18160.42510.0505-0.03570.23940.00730.301332.110315.450124.9859
38.0962.76320.89645.95510.83753.9036-0.27530.35090.8319-0.7789-0.06440.1607-0.3127-0.68420.29060.24850.054-0.01140.313-0.00770.279113.246611.623617.5433
47.13862.96653.28221.26441.13535.7809-0.1748-0.02651.87810.0312-0.05190.4832-0.2415-2.16170.8910.6378-0.1292-0.3141.73590.17140.5882-7.75368.797515.7525
52.85341.65281.29183.82180.35840.6258-0.52151.3376-0.3934-0.81650.61960.20931.3399-0.8775-0.12120.6935-0.3817-0.01831.057-0.18510.59734.3072-2.043711.5591
66.0754.60322.80099.20832.57233.74160.5449-0.2978-1.13480.6421-0.0221-0.27431.9307-1.691-0.50640.7856-0.3207-0.01380.7277-0.01190.46444.3753-1.805522.5934
77.49163.73142.9166.5413-2.53224.5133-0.1386-0.171.33170.50030.48940.7378-0.1087-1.6861-0.22190.38630.00670.1221.2213-0.06870.5767-2.20628.903323.3191
82.0349-1.37982.18245.9888-0.43028.04480.05020.06380.907-0.0075-0.03530.2618-0.9986-0.68240.08020.3060.03380.00820.5227-0.0310.47768.86911.372929.1585
92.7831.9529-2.79312.1798-2.26267.5333-0.19810.154-0.2504-0.12890.10340.3730.5056-0.63590.15430.279-0.0243-0.00950.199-0.010.437919.65082.310226.4196
105.90990.2491-2.56932.43130.40057.78060.0543-0.59680.12850.216-0.04530.0460.00130.1820.01720.2531-0.01520.00010.1876-0.0260.300723.85069.542232.3469
114.72584.73031.17195.7282.88993.2497-0.3697-0.02531.6277-0.22330.29271.5799-0.6077-1.11880.24480.56070.0305-0.07940.7291-0.06321.02915.319118.724920.6977
127.7351-0.5454.13794.8108-0.94776.43320.11940.97950.1548-1.3210.1003-0.8716-0.51941.1699-0.39081.0365-0.15080.15320.4473-0.1440.32632.385322.5416-2.5574
130.76551.35630.68132.49870.97180.9249-0.09940.3731-0.1965-1.5129-0.07470.19480.6548-0.50260.11221.5584-0.191-0.12890.6144-0.02840.338828.5148.0752-6.6602
145.3181-1.4703-1.57630.94942.34847.41670.1037-0.1658-0.3209-1.1918-0.214-0.0436-0.29520.42820.03440.57160.0485-0.02990.2809-0.02470.196531.924514.3037.5885
155.7489-2.3108-0.47868.6475-0.07155.7317-0.1540.0398-0.0002-0.4024-0.2283-0.3854-0.38840.67570.47130.3106-0.07240.01930.3220.0610.227235.192517.269913.3154
167.58293.9328-0.87567.6636-1.18527.96270.86330.9423-0.6908-0.67480.03222.20890.6361-0.8679-0.77650.5272-0.0469-0.14120.39740.01660.67721.03229.90765.7503
179.24910.6862-2.70624.17884.08675.23630.22920.96720.277-1.645-0.56371.2538-0.4039-0.34880.39940.8113-0.0154-0.12380.3328-0.00270.331223.276317.05170.1388
183.5339-1.0478-3.06087.23234.06264.33420.1464-0.1444-0.1433-1.61150.13950.19160.27180.244-0.11540.82550.08230.04310.28540.01450.320928.643620.17081.1202
196.37231.87-3.57196.51722.30153.89840.32740.30860.37611.11890.06120.4198-0.0373-0.637-0.34540.47910.02790.0620.25620.01210.29121.874825.999715.4193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 97 through 107 )B97 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid -50 through -41 )A-50 - -41
3X-RAY DIFFRACTION3chain 'A' and (resid -40 through -21 )A-40 - -21
4X-RAY DIFFRACTION4chain 'A' and (resid -20 through 29 )A-20 - 29
5X-RAY DIFFRACTION5chain 'A' and (resid 30 through 53 )A30 - 53
6X-RAY DIFFRACTION6chain 'A' and (resid 54 through 70 )A54 - 70
7X-RAY DIFFRACTION7chain 'A' and (resid 71 through 86 )A71 - 86
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 98 )A87 - 98
9X-RAY DIFFRACTION9chain 'A' and (resid 99 through 122 )A99 - 122
10X-RAY DIFFRACTION10chain 'A' and (resid 123 through 159 )A123 - 159
11X-RAY DIFFRACTION11chain 'A' and (resid 160 through 169 )A160 - 169
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 8 )B1 - 8
13X-RAY DIFFRACTION13chain 'B' and (resid 9 through 20 )B9 - 20
14X-RAY DIFFRACTION14chain 'B' and (resid 21 through 30 )B21 - 30
15X-RAY DIFFRACTION15chain 'B' and (resid 31 through 45 )B31 - 45
16X-RAY DIFFRACTION16chain 'B' and (resid 46 through 56 )B46 - 56
17X-RAY DIFFRACTION17chain 'B' and (resid 57 through 65 )B57 - 65
18X-RAY DIFFRACTION18chain 'B' and (resid 66 through 81 )B66 - 81
19X-RAY DIFFRACTION19chain 'B' and (resid 82 through 96 )B82 - 96

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