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- PDB-4yug: Multiconformer synchrotron model of CypA at 100 K -

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Basic information

Entry
Database: PDB / ID: 4yug
TitleMulticonformer synchrotron model of CypA at 100 K
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilin
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsKeedy, 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.
CitationJournal: 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
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A


Theoretical massNumber of molelcules
Total (without water)18,0371
Polymers18,0371
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.240, 51.910, 88.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.48→38.085 Å / Num. obs: 32657 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.07
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 1.57 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.48→38.085 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1833 1028 3.15 %
Rwork0.1327 --
obs0.1343 32627 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→38.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 338 1604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082025
X-RAY DIFFRACTIONf_angle_d1.1632801
X-RAY DIFFRACTIONf_dihedral_angle_d13.088774
X-RAY DIFFRACTIONf_chiral_restr0.079285
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5580.26841470.20354507X-RAY DIFFRACTION100
1.558-1.65560.22311430.16044482X-RAY DIFFRACTION100
1.6556-1.78350.18981470.13294509X-RAY DIFFRACTION100
1.7835-1.9630.18261450.11694477X-RAY DIFFRACTION99
1.963-2.2470.15331460.11394504X-RAY DIFFRACTION99
2.247-2.83080.17121470.13694520X-RAY DIFFRACTION98
2.8308-38.09780.18381530.13014600X-RAY DIFFRACTION96

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