Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18036.50 
• Atom Count: 2003 
• Residue Count: 165 
• Unique protein chains: 1

4YUN

Multiconformer synchrotron model of CypA at 310 K

• DOI: 10.2210/pdb4YUN/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-03-18 Released: 2015-10-14 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.150 
• R-Value Work: 0.117 

Literature

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

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.

(2015) Elife 4: --

• PubMed: 26422513 
• DOI: 10.7554/eLife.07574
• Primary Citation of Related Structures:  
  4YUP, 4YUO, 4YUM, 4YUL, 4YUK, 4YUJ, 4YUI, 4YUH, 4YUG


• PubMed Abstract: 
  

Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180--240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

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Organizational Affiliation: 

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA (CYPA) EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Go to Gene View: PPIA Go to UniProtKB:  P62937

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.150 
• R-Value Work: 0.117 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 42.850	α = 90.00
b = 52.580	β = 90.00
c = 89.410	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-18 
• Released Date: 2015-10-14 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2015-10-14
  Type: Initial release