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Title: Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination

Abstract

In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019)Proc Natl Acad Sci USA, 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure.

Authors:
ORCiD logo [1];  [1];  [1]; ORCiD logo [1]
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  1. Stanford Univ. School of Medicine, Stanford, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1532382
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 116; Journal Issue: 22; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Ufimtsev, Ivan S., Almagor, Lior, Weis, William I., and Levitt, Michael. Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination. United States: N. p., 2019. Web. doi:10.1073/pnas.1821513116.
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Ufimtsev, Ivan S., Almagor, Lior, Weis, William I., & Levitt, Michael. Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination. United States. doi:10.1073/pnas.1821513116.
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Ufimtsev, Ivan S., Almagor, Lior, Weis, William I., and Levitt, Michael. Tue . "Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination". United States. doi:10.1073/pnas.1821513116. https://www.osti.gov/servlets/purl/1532382.
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@article{osti_1532382,
title = {Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination},
author = {Ufimtsev, Ivan S. and Almagor, Lior and Weis, William I. and Levitt, Michael},
abstractNote = {In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019)Proc Natl Acad Sci USA, 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure.},
doi = {10.1073/pnas.1821513116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 22,
volume = 116,
place = {United States},
year = {2019},
month = {5}
}
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Journal Article:
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DOI:  10.1073/pnas.1821513116
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Figures / Tables:

Figure 1 Figure 1: Statistics of the Lgl2 models progressively constructed in the solution process started with the best MR model found automatically by our unsupervised refinement pipeline in the pool of 50 MR solutions. Blue, pink, and brown bars represent the relative number of atoms, residues, and sequence identities (structurally alignedmore » identical amino acids) with respect to the final solution. Black line denotes RMSD from the solution plotted on a different scale. The “auto_x” models were built in Coot and refined by our unsupervised refinement code for ∼60 macrocycles each. Structure “auto_9” had phases of good quality, sufficient for standard manual processing. This model was finalized manually with Coot and phenix.refine in 40 build−refine iterations. The dashed lines represent summarized statistics of these runs.« less
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    • Kumar, Pranav; Dalal, Vikram; Sharma, Nidhi
    • Metallomics, Vol. 12, Issue 2
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    Unsupervised determination of protein crystal structures
    journal, May 2019

    • Ufimtsev, Ivan S.; Levitt, Michael
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 22
    • DOI: 10.1073/pnas.1821512116
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