+Open data
-Basic information
Entry | Database: PDB / ID: 4yun | ||||||
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Title | Multiconformer synchrotron model of CypA at 310 K | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | ISOMERASE / Cyclophilin | ||||||
Function / homology | Function and homology information negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / integrin binding / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. ...Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Mori, R.A. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S. | ||||||
Citation | Journal: Elife / Year: 2015 Title: Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. ...Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Alonso-Mori, R. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, S.M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yun.cif.gz | 150.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yun.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 4yun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yun_validation.pdf.gz | 410.9 KB | Display | wwPDB validaton report |
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Full document | 4yun_full_validation.pdf.gz | 410.8 KB | Display | |
Data in XML | 4yun_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4yun_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/4yun ftp://data.pdbj.org/pub/pdb/validation_reports/yu/4yun | HTTPS FTP |
-Related structure data
Related structure data | 4yugC 4yuhC 4yuiC 4yujC 4yukC 4yulC 4yumC 4yuoC 4yupC 2cplS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format. |
-Data collection
Diffraction | Mean temperature: 310 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→25.222 Å / Num. obs: 28291 / % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.26 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.273 / Mean I/σ(I) obs: 1.45 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CPL Resolution: 1.58→25.222 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→25.222 Å
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Refine LS restraints |
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LS refinement shell |
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