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- PDB-7u0u: Crystal Structure of a Aspergillus fumigatus Calcineurin A - Calc... -

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Basic information

Entry
Database: PDB / ID: 7u0u
TitleCrystal Structure of a Aspergillus fumigatus Calcineurin A - Calcineurin B fusion bound to FKBP12 and FK-506
Components
  • Peptidylprolyl isomeraseProlyl isomerase
  • Serine/threonine-protein phosphatase 2B catalytic subunit,AsfuA.00174.a.TQ11 + AsfuA.01011.a.TR11
KeywordsANTIFUNGAL PROTEIN / SSGCID / Calcineurin / CnA / CnB / FKBP12 / peptidyl prolyl cis-trans isomerase / phosphatase / FK-506 / Tacrolimus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


calmodulin-dependent protein phosphatase activity / calcineurin complex / calcineurin-mediated signaling / fungal-type cell wall organization / myosin phosphatase activity / protein-serine/threonine phosphatase / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calmodulin binding / metal ion binding / cytoplasm
Similarity search - Function
Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / EF hand / 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 ...Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / EF hand / 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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / PHOSPHATE ION / Peptidylprolyl isomerase / Calcineurin subunit B / Serine/threonine-protein phosphatase 2B catalytic subunit
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFox III, D. / Abendroth, 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit,AsfuA.00174.a.TQ11 + AsfuA.01011.a.TR11
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3509
Polymers44,0962
Non-polymers1,2547
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-67 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.010, 83.700, 137.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase 2B catalytic subunit,AsfuA.00174.a.TQ11 + AsfuA.01011.a.TR11 / Calmodulin-dependent calcineurin A subunit


Mass: 29821.238 Da / Num. of mol.: 1 / Fragment: AsfuA.00174.a.TQ11 + AsfuA.01011.a.TR11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100
Gene: cnaA, AFUA_5G09360, CNMCM8057_008799, CNMCM8686_005215
Plasmid: AsfuA.00174.a.TQ11 + AsfuA.01011.a.TR11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4WUR1, UniProt: A0A8H4MJX9, protein-serine/threonine phosphatase
#2: Protein Peptidylprolyl isomerase / Prolyl isomerase


Mass: 14275.007 Da / Num. of mol.: 1 / Fragment: AsfuA.18272.a / Mutation: P90G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_03547 / Plasmid: AsfuA.18272.a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A229WIB4, peptidylprolyl isomerase

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Non-polymers , 5 types, 180 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506 / Tacrolimus


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: RigakuReagents JCSG+ C6: 0.1M Phosphate-citrate (rather sodium phosphate dibasic / citric acid) pH4.2, 40% PEG300, AsfuA.18272.a.JA12.PD38437 at 20mg/ml + FK-506 (Purified from SEC): cryo: ...Details: RigakuReagents JCSG+ C6: 0.1M Phosphate-citrate (rather sodium phosphate dibasic / citric acid) pH4.2, 40% PEG300, AsfuA.18272.a.JA12.PD38437 at 20mg/ml + FK-506 (Purified from SEC): cryo: direct: tray 318723c6, puck enw1-2.

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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: 1.9→50 Å / Num. obs: 34390 / % possible obs: 99.6 % / Redundancy: 5.921 % / Biso Wilson estimate: 38.538 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 0.941 / Net I/σ(I): 19.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.954.3850.572.3424850.7650.64998.5
1.95-25.460.4343.5824650.8870.482100
2-2.066.1440.3215.2823880.9510.351100
2.06-2.126.1930.2496.8223220.9630.272100
2.12-2.196.1630.2018.3522380.9750.22100
2.19-2.276.1710.16910.0322080.9820.185100
2.27-2.366.1760.13512.1820830.9890.148100
2.36-2.456.1650.11214.4920420.9920.123100
2.45-2.566.1720.09517.2919510.9950.104100
2.56-2.696.1410.07820.5718770.9960.08599.9
2.69-2.836.1350.06424.0317600.9970.0799.9
2.83-36.0580.05428.4717070.9980.05999.9
3-3.216.0630.04433.9415810.9980.04899.7
3.21-3.476.0040.03840.0214670.9990.04299.7
3.47-3.85.9330.03442.3513750.9990.03799.3
3.8-4.255.9490.0346.1612460.9990.03399.3
4.25-4.915.9210.02749.311040.9990.0399.5
4.91-6.015.9360.02647.529370.9990.02998.5
6.01-8.55.870.02448.627360.9990.02798
8.5-505.3540.02249.744180.9990.02493.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.75 Å43.36 Å
Translation2.75 Å43.36 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tz7

6tz7


Resolution: 1.9→39.13 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 1997 5.81 %
Rwork0.169 32387 -
obs0.1707 34384 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 79 173 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642552
X-RAY DIFFRACTIONf_angle_d0.84793480
X-RAY DIFFRACTIONf_chiral_restr0.0512395
X-RAY DIFFRACTIONf_plane_restr0.0055451
X-RAY DIFFRACTIONf_dihedral_angle_d12.8979962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27651400.2552264X-RAY DIFFRACTION98.4
1.95-20.23451410.21842289X-RAY DIFFRACTION100
2-2.060.2251400.18832288X-RAY DIFFRACTION99.88
2.06-2.130.22021420.18222297X-RAY DIFFRACTION100
2.13-2.20.24251410.18192296X-RAY DIFFRACTION100
2.2-2.290.2161410.18582290X-RAY DIFFRACTION99.96
2.29-2.390.21051440.16872310X-RAY DIFFRACTION100
2.39-2.520.20691420.17052307X-RAY DIFFRACTION99.96
2.52-2.680.21931420.17692315X-RAY DIFFRACTION99.96
2.68-2.880.21061430.18292313X-RAY DIFFRACTION99.92
2.88-3.170.23671430.17972315X-RAY DIFFRACTION99.84
3.17-3.630.1961440.16872332X-RAY DIFFRACTION99.56
3.63-4.580.15831450.13882349X-RAY DIFFRACTION99.4
4.58-39.130.1781490.16052422X-RAY DIFFRACTION97.83
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)
13.072581353080.104305908602-0.7382879693425.07810685508-4.081210128388.923366106830.129398259993-0.04999464311080.120088489869-0.0467680580463-0.0134019046753-0.002204265095420.0900479162993-0.114965191795-0.08396234675860.2211207204510.0252720964297-0.01857425672120.212775800843-0.08627540404620.232034793781-26.1853889986-10.1335044023-20.7897801849
24.518770413511.885392935530.7375885744177.8857529169-1.188343707522.146850046750.229795265202-1.751557911040.1215960632671.35264318721-0.242758081104-0.09761222708640.54428827231-0.520374354980.1278976061140.813627111335-0.07226024002370.06881470434351.141258717110.09379671427760.479635791728-26.4237022319-15.11807229937.61580717159
30.9429158870162.00755702087-0.4329474144227.80277441141-3.594766799932.241563073880.238883197028-1.8009669642-1.589506779850.622056315310.0368398793683-0.08498101300671.642465640210.605327596321-0.3475749746470.9751399436330.3359502055920.1561897283631.035694678870.4911480606060.889170962187-18.0003849729-27.78392017120.34811565524
43.66987145109-0.000522452026298-0.525398090091.724811398930.3772833025723.929573819550.0208684442723-0.7095894716110.03761933375190.2772961058890.0273856843733-0.1329719338080.176509102710.270439339115-0.05210117726290.2377571726460.0442539072664-0.03714981999030.361416095886-0.09530671857230.243480898708-17.4142458163-10.2104984265-14.3224988403
54.91935870716-2.8753698898-1.319171293292.143509677330.7015835166675.47248474119-0.308841068088-0.4847640807070.02855139001670.2527274675010.05816000456660.6884396197280.0423433708914-0.4570978227560.266466957930.3451107029920.01015965599750.003149228654150.461983746601-0.1521695515860.340761399541-30.6982883081-4.43907590923-10.6192553995
62.49512471307-3.65926292794-4.307089072045.549431546166.493167376197.596381431340.06741305863470.4929296206230.120358942248-0.417812899755-0.3586432139730.862815007477-0.546964025671-1.227945285310.4943005213770.32621316818-0.0372394967294-0.08089537430380.320622586341-0.04425752711540.373162637494-48.1599663635-18.6601342641-35.654163356
75.176844877141.109337097322.899289892395.302237956061.200394363546.523542588540.11976243549-0.150582888487-0.5169731914610.345839363474-0.234070179136-0.163626879220.849154653738-0.4404296741530.07633927902450.309243628977-0.0380233227394-0.04964233574370.204094481864-0.03061207912940.386975436969-41.6061181938-31.6633020403-32.8702183848
84.795887788441.15287381583-1.430843661023.873854493452.375897608812.547420271450.1155770460170.2615899378620.474853553814-0.2464825316840.0720450013467-0.479445037261-0.2314733908620.0648275421204-0.1777132652640.270211116551-0.0195256226885-0.02191932441550.264806597192-0.03209562379410.19500716174-36.2371846524-12.0759783983-34.4167219003
98.598645421-2.859365576321.279558837123.772986608-4.663855040856.670731470340.1256320394860.2602585468640.136579180318-0.3481113695780.047126079391-0.3402977569530.2323663497050.630355831813-0.208268349260.356381743367-0.0320201177028-0.01654933306480.374954647041-0.1119483905470.259264568523-27.5477357763-15.4698892468-38.0767954961
106.58632965817-0.603901608396-4.457887504697.548108396130.04392073928246.379585170160.00872920032041-0.449142812113-0.5243036829810.6288490996470.0344506983935-0.5009282045240.4648630794670.296708227853-0.02078839702060.291611156248-0.00150346911558-0.1048882245290.242844815977-0.0182837286990.319199019314-34.0329123886-22.3775096219-24.3218453795
115.507973079995.867915117886.134569156496.312898313536.587205234736.892685484110.347923062727-0.801473561835-0.4462805158510.902253386601-0.2960614135810.2624785355370.605399722147-0.7263698313720.01183439278950.335620403422-0.00856840271208-0.03692295704160.2851721199690.02603138849410.291637327606-42.8072513935-21.5176173762-26.6278642611
122.266871069820.268565535870.3516408387268.557496172215.9994595634.43370655770.006198125715930.0982832294484-0.1717479453220.176223747596-0.0664000178110.2639114335990.298930328945-0.1555896525190.101520306630.246206653937-0.00476148158458-0.01444622661190.2036843405080.02142702089810.216042339304-43.1261919313-15.4862371681-28.5484328123
132.57122867918-0.1965911755950.3643377824669.366053284453.720454419063.49387207377-0.07170298804590.15807234460.0072699348314-0.3025457830460.1534476167220.0823709841716-0.2229576198660.0123081719002-0.1009882251590.179206401431-0.01856242191110.01105406965650.1872758963260.01311303603260.19600663138-38.6571719354-11.9045916764-30.2134147115
147.03121666899-0.6723919676272.990131855123.278756388-3.041738174463.65885590545-0.227467984440.232296755656-0.858464474763-0.5621453449740.519221275402-0.582438655075-0.2319928788770.910309371315-0.2603479361210.5493915340320.00879706912922-0.07288947453860.538285776141-0.188708050980.656797129005-31.6410807174-32.2822773656-35.6560538539
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -50 through -20 )AA-50 - -201 - 31
22chain 'A' and (resid -19 through 52 )AA-19 - 5232 - 54
33chain 'A' and (resid 53 through 66 )AA53 - 6655 - 68
44chain 'A' and (resid 67 through 178 )AA67 - 17869 - 180
55chain 'A' and (resid 179 through 193 )AA179 - 193181 - 195
66chain 'B' and (resid 1 through 9 )BH1 - 91 - 9
77chain 'B' and (resid 10 through 21 )BH10 - 2110 - 21
88chain 'B' and (resid 22 through 39 )BH22 - 3922 - 39
99chain 'B' and (resid 40 through 46 )BH40 - 4640 - 46
1010chain 'B' and (resid 47 through 57 )BH47 - 5747 - 57
1111chain 'B' and (resid 58 through 66 )BH58 - 6658 - 66
1212chain 'B' and (resid 67 through 86 )BH67 - 8667 - 86
1313chain 'B' and (resid 87 through 107 )BH87 - 10787 - 107
1414chain 'B' and (resid 108 through 112 )BH108 - 112108 - 112

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