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- PDB-4yuj: Multiconformer synchrotron model of CypA at 240 K -

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Basic information

Entry
Database: PDB / ID: 4yuj
TitleMulticonformer synchrotron model of CypA at 240 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 / negative regulation of viral life cycle / 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 / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / 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 / viral release from host cell / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / 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 / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.42 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 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.040, 53.220, 88.630
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.: 216 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
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: 240 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: 1.42→34.055 Å / Num. obs: 38881 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.86
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.66 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CPL

2cpl


Resolution: 1.42→34.055 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 1218 3.13 %
Rwork0.1255 --
obs0.1265 38879 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→34.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 216 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091837
X-RAY DIFFRACTIONf_angle_d1.1972543
X-RAY DIFFRACTIONf_dihedral_angle_d11.161709
X-RAY DIFFRACTIONf_chiral_restr0.077255
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4201-1.47690.3041300.26254031X-RAY DIFFRACTION96
1.4769-1.54420.22151300.20374136X-RAY DIFFRACTION100
1.5442-1.62560.1771340.15494158X-RAY DIFFRACTION100
1.6256-1.72740.161380.12924172X-RAY DIFFRACTION100
1.7274-1.86080.15651310.12164181X-RAY DIFFRACTION100
1.8608-2.0480.1511380.11134192X-RAY DIFFRACTION100
2.048-2.34430.14161340.10944191X-RAY DIFFRACTION99
2.3443-2.95330.16911420.12334234X-RAY DIFFRACTION99
2.9533-34.06450.13291410.11374366X-RAY DIFFRACTION98

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