5KV3

Human cyclophilin A at 278K, Data set 5

Summary for 5KV3

• Entry DOI: 10.2210/pdb5kv3/pdb
• Related: 5KUL 5KUN 5KUO 5KUQ 5KUR 5KUS 5KUU 5KUV 5KUW 5KUZ 5KV0 5KV1 5KV2 5KV4 5KV5 5KV6 5KV7
• Descriptor: Peptidyl-prolyl cis-trans isomerase A (2 entities in total)
• Functional Keywords: conformational variation, radiation damage, isomerase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 17905.31

Authors

Russi, S.,Gonzalez, A.,Kenner, L.R.,Keedy, D.A.,Fraser, J.S.,van den Bedem, H. (deposition date: 2016-07-13, release date: 2016-08-10, Last modification date: 2023-10-04)

Primary citation

Russi, S.,Gonzalez, A.,Kenner, L.R.,Keedy, D.A.,Fraser, J.S.,van den Bedem, H.
Conformational variation of proteins at room temperature is not dominated by radiation damage.
J Synchrotron Radiat, 24:73-82, 2017

PubMed Abstract: Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 10 Gy at 100 K and 10 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

PubMed: 28009548
DOI: 10.1107/S1600577516017343

Experimental method

X-RAY DIFFRACTION (1.7 Å)