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Yorodumi- PDB-6tz8: Crystal structure of Cryptococcus neoformans Calceineurin A, Calc... -
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-Basic information
Entry | Database: PDB / ID: 6tz8 | ||||||
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Title | Crystal structure of Cryptococcus neoformans Calceineurin A, Calcineurin B, and FKBP12 with FK-506 | ||||||
Components |
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Keywords | Hydrolase/Isomerase/Calcium Binding / Calcineurin A / CnA / CnB / FKBP12 / FK-506 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Hydrolase-Isomerase-Calcium Binding complex | ||||||
Function / homology | Function and homology information mitotic actomyosin contractile ring, intermediate layer / positive regulation of mitotic division septum assembly / fungal-type cell wall organization or biogenesis / positive regulation of mitotic actomyosin contractile ring contraction / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / calcineurin complex ...mitotic actomyosin contractile ring, intermediate layer / positive regulation of mitotic division septum assembly / fungal-type cell wall organization or biogenesis / positive regulation of mitotic actomyosin contractile ring contraction / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / calcineurin complex / calcineurin-mediated signaling / protein-serine/threonine phosphatase / cellular response to calcium ion / ferric iron binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein localization to nucleus / calmodulin binding / intracellular signal transduction / calcium ion binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptococcus neoformans var. grubii serotype A (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents. Authors: Juvvadi, P.R. / Fox 3rd, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M.C. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. ...Authors: Juvvadi, P.R. / Fox 3rd, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M.C. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / Trzoss, M. / Li, X. / Lee, S.C. / Chen, Y.L. / Mutz, M. / Spicer, L.D. / Schumacher, M.A. / Heitman, J. / Steinbach, W.J. #1: Journal: Nat Commun / Year: 2019 Title: Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents Authors: Juvvadi, P.R. / Fox III, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / ...Authors: Juvvadi, P.R. / Fox III, D. / Bobay, B.G. / Hoy, M.J. / Gobeil, S.M. / Venters, R.A. / Chang, Z. / Lin, J.J. / Averette, A.F. / Cole, D.C. / Barrington, B.C. / Wheaton, J.D. / Ciofani, M. / Trzoss, M. / Li, X. / Lee, S.C. / Chen, Y. / Mutz, M. / Spicer, L.D. / Schumacher, M.A. / Heitman, J. / Steinbach, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tz8.cif.gz | 275.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tz8.ent.gz | 214.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tz8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6tz8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6tz8_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 6tz8_validation.cif.gz | 62.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/6tz8 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/6tz8 | HTTPS FTP |
-Related structure data
Related structure data | 5b8iC 6tz6C 6tz7C 1tcoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 45253.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNA1, CNAG_04796 / Plasmid: pEMB44 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tni References: UniProt: O42773, protein-serine/threonine phosphatase #2: Protein | Mass: 19700.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00888 / Plasmid: pEMB44 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tni / References: UniProt: J9VL81 #3: Protein | Mass: 13333.070 Da / Num. of mol.: 2 / Mutation: S9K, K14V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: FRR1, CNAG_03682 / Plasmid: pEMB44 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tni / References: UniProt: O94746, peptidylprolyl isomerase |
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-Non-polymers , 6 types, 26 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CA / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: CRYPTOCOCCUS NEOFORMANS CALCINEURIN A (CRNEC.00174.A.EX14), CALCINEURIN B (CRNEC.01011.A.FX11), AND FKBP12 (CRNEC.18272.A.DB13) WITH FK-506 IN 25MM MES PH6.4, 150MM NACL, 0.5MM TCEP, 5MM ...Details: CRYPTOCOCCUS NEOFORMANS CALCINEURIN A (CRNEC.00174.A.EX14), CALCINEURIN B (CRNEC.01011.A.FX11), AND FKBP12 (CRNEC.18272.A.DB13) WITH FK-506 IN 25MM MES PH6.4, 150MM NACL, 0.5MM TCEP, 5MM CACL2, 5UM FK506 WAS CRYSTALLIZED AT 9.38MG/ML AGAINST MORPHEUS II CONDITION A3 CONTAINING 30MM LITHIUM SULFATE, 30MM SODIUM SULFATE, 30MM POTASSIUM SULFATE, 0.1M MOPSO/0.1M BIS-TRIS PH6.5, 10% W/V PEG8000 AND 20% W/V 1, 5 PENTANEDIOL. CRYSTALS WERE DIRECTLY CRYO-PROTECTED IN 20% ETHYLENE GLYCOL PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2016 / Details: BERYLLIUM LENSES |
Radiation | Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 29795 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.215 / Net I/σ(I): 8.62 |
Reflection shell | Resolution: 3.3→3.39 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2188 / CC1/2: 0.918 / Rrim(I) all: 0.642 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TCO Resolution: 3.3→44.57 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→44.57 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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