Open Dataset XSSQ87OY

PCTrip (dodecameric tetrahedral protein cage triple mutant) Salt and pH studies.


The Yeates lab designed a dodecomeric tetrahedral protien cage (PC) with a total mass of 600kDa. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain (sequence available in this entry). This data set is from a triple mutant (PCtrip) that imparted greater symmetry in the cage as observed in cryoEM and crystallography over the original design and reported in previous publications (Padilla, Yeates et al PNAS 2001)(Lai, Yeates et al, JACS 2013). High-throughput small-angle x-ray scattering (SAXS) comprehensively studied conformation and assembly under varying pH and NaCl concentrations. This set includes pH steps from 4 through to 11 and NaCl concentrations 10, 100, 300 and 500mM. In total, there were therefore 32 measurements. The data were reported in a paper titled "Designing and defining dynamic protein cage nanoassemblies in solution" by Lai, Hura, Tainer, Yeates et al in Science Advances, 2016 (DOI: 10.1126/sciadv.1501855) Specifically, our results probed the influence of salt concentration and pH on symmetry, stability and structural adaptability.

Experimental description:

The full amino acid sequence of the PCTrip Monomer is: MPFITVGQENSTSIDLYYEDHGTGTPVVLIHGFPLSGHSWERQSAALLDAGYRVITYDRRGFGQSSQPTTGYDYDTFAADLNTVLETLDLQDAVLVGFSMGTGEVARYVSSYGTARIAAVAFLASLEPFLLKTDDNPDGAAPQEFFDGIVAAVKADRYAFYTGFFNDFYNLDENLGTRISEEAVRNSWNTAASGGFFAAAAAPTTWYTDFRADIPRIDVPALILHGTGDRTLPIENTARVFHKALPSAEYVEVEGAPHGLLWTHAEEVNTALLAFLAKAQEAQKQKLLTEVETYVLSIIPSGPLKAEIAQRLEDVFAGKNTDLEVLMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDKAVKLYRKLKREITFHGAKEISLSYSAGALASCMGLIYNRMGAVTTEVAFGLVCATCEQIADSQHRSHRQLEHHHHHH Stock protein was ~30 mg/ml in 20 mM Tris (pH 8.0) and 100 mM NaCl. The sample was dialyzed over night in the desired buffer condition. Buffer was modified to maintain specific pH values: pH 4 to 6, 7 to 9, and 10 to 11 were prepared in MES, tris, and CAPS, respectively. Thus, the initial protein sample in any given well on a plate was identical but then modified by the changing solution environment. Protein concentration for measurement was held constant between wells at ~2.2 mg/ml. The final concentration after dialysis was not measured so if protein aggregation occurred, reducing concentration, this was not corrected. Out of the 32 measurements that were conducted, only 27 are provided in this set. The five missing conditions were conditions that created aggregates. Also the 300mM at pH 9 condition was not included due to issues during the experiment. Data was collected at the SIBYLS beamline at the Advanced Light Source, Lawrence Berkeley National Lab. A liquid handler pulled samples from a 96 well plate for collection.

File description:

Each file name designates the concentration of NaCl in mM and the pH. A file named 10mM_pH7_PCTrip.dat is PCTrip in 10mM NaCl at pH7.

Data collection technique:



Sample to Detector Distance

Created: 2022-05-24

Updated: 2022-05-24

Submitting Author:

Greg Hura

Lawrence Berkeley National Laboratory, The SIBYLS Beamline

United States of America

[email protected]



Project Leader:

Greg Hura

[email protected]

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Complete Set of SAXS Data Files:

The complete SAXS dataset is downloadable as a zip file.

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Sample SAXS Data Files (total 26):

These are individual SAXS data files that are included in the complete dataset, but are available separately for quick download as examples of what is contained in the zip file.

Supplemental Data and Supporting Materials (total 1):

These data and materials may include X-ray crystal structure coordinates, multi-angle light scattering data, .etc. It may also include additional details or methods pertaining to the SAXS experiments, or the researcher's interpretations of the results.

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  • Macromolecule 1: PCTrip
    • Sample Full Name: Triple Mutant over the original designed tetrahedral protein cage
    • Sample Type: Protein
    • Source Organism:
    • Source Organism NCBI Taxonomy ID:
    • Expression System:
    • Expression NCBI Taxonomy ID:
    • Sequence or Chemical Formula: