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Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.

Protein science : a publication of the Protein Society

Wang J.
PMID: 28244185
Protein Sci. 2017 May;26(5):1012-1023. doi: 10.1002/pro.3145. Epub 2017 Mar 07.

In the residual electron density map of a fully refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences...

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Wang J. Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent. Protein Sci. 2017;26(5):1012-1023doi: 10.1002/pro.3145.
Wang, J. (2017). Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent. Protein science : a publication of the Protein Society, 26(5), 1012-1023. https://doi.org/10.1002/pro.3145
Wang, Jimin. "Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent." Protein science : a publication of the Protein Society vol. 26,5 (2017): 1012-1023. doi: https://doi.org/10.1002/pro.3145
Wang J. Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent. Protein Sci. 2017 May;26(5):1012-1023. doi: 10.1002/pro.3145. Epub 2017 Mar 07. PMID: 28244185; PMCID: PMC5405434.
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SDADB: a functional annotation database of protein structural domains.

Database : the journal of biological databases and curation

Zeng C, Zhan W, Deng L.
PMID: 29961821
Database (Oxford). 2018 Jan 01;2018. doi: 10.1093/database/bay064.

Annotating functional terms with individual domains is essential for understanding the functions of full-length proteins. We describe SDADB, a functional annotation database for structural domains. SDADB provides associations between gene ontology (GO) terms and SCOP domains calculated with an...

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Zeng C, Zhan W, Deng L. SDADB: a functional annotation database of protein structural domains. Database (Oxford). 2018;2018doi: 10.1093/database/bay064.
Zeng, C., Zhan, W., & Deng, L. (2018). SDADB: a functional annotation database of protein structural domains. Database : the journal of biological databases and curation, 2018. https://doi.org/10.1093/database/bay064
Zeng, Cheng, et al. "SDADB: a functional annotation database of protein structural domains." Database : the journal of biological databases and curation vol. 2018 (2018). doi: https://doi.org/10.1093/database/bay064
Zeng C, Zhan W, Deng L. SDADB: a functional annotation database of protein structural domains. Database (Oxford). 2018 Jan 01;2018. doi: 10.1093/database/bay064. PMID: 29961821; PMCID: PMC6025185.
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2.

Proceedings of the National Academy of Sciences of the United States of America

Schmidt SH, Weng JH, Aoto PC, Boassa D, Mathea S, Silletti S, Hu J, Wallbott M, Komives EA, Knapp S, Herberg FW, Taylor SS.
PMID: 34088839
Proc Natl Acad Sci U S A. 2021 Jun 08;118(23). doi: 10.1073/pnas.2100844118.

To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and...

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Schmidt SH, Weng JH, Aoto PC, et al. Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A. 2021;118(23)doi: 10.1073/pnas.2100844118.
Schmidt, S. H., Weng, J. H., Aoto, P. C., Boassa, D., Mathea, S., Silletti, S., Hu, J., Wallbott, M., Komives, E. A., Knapp, S., Herberg, F. W., & Taylor, S. S. (2021). Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proceedings of the National Academy of Sciences of the United States of America, 118(23), . https://doi.org/10.1073/pnas.2100844118
Schmidt, Sven H, et al. "Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2." Proceedings of the National Academy of Sciences of the United States of America vol. 118,23 (2021). doi: https://doi.org/10.1073/pnas.2100844118
Schmidt SH, Weng JH, Aoto PC, Boassa D, Mathea S, Silletti S, Hu J, Wallbott M, Komives EA, Knapp S, Herberg FW, Taylor SS. Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A. 2021 Jun 08;118(23). doi: 10.1073/pnas.2100844118. PMID: 34088839; PMCID: PMC8201809.
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Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains.

Scientific reports

Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.
PMID: 27612191
Sci Rep. 2016 Sep 09;6:33112. doi: 10.1038/srep33112.

Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects...

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Chugunov AO, Volynsky PE, Krylov NA, et al. Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep. 2016;6:33112doi: 10.1038/srep33112.
Chugunov, A. O., Volynsky, P. E., Krylov, N. A., Nolde, D. E., & Efremov, R. G. (2016). Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Scientific reports, 633112. https://doi.org/10.1038/srep33112
Chugunov, Anton O, et al. "Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains." Scientific reports vol. 6 (2016): 33112. doi: https://doi.org/10.1038/srep33112
Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG. Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep. 2016 Sep 09;6:33112. doi: 10.1038/srep33112. PMID: 27612191; PMCID: PMC5017144.
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Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain.

Molecules and cells

Park SS, Lee S, Rhee DK.
PMID: 33795535
Mol Cells. 2021 Mar 31;44(3):179-185. doi: 10.14348/molcells.2021.2235.

Vancomycin response regulator (VncR) is a pneumococcal response regulator of the VncRS two-component signal transduction system (TCS) of Streptococcus pneumoniae. VncRS regulates bacterial autolysis and vancomycin resistance. VncR contains two different functional domains, the N-terminal receiver domain and C-terminal...

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Park SS, Lee S, Rhee DK. Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain. Mol Cells. 2021;44(3):179-185doi: 10.14348/molcells.2021.2235.
Park, S. S., Lee, S., & Rhee, D. K. (2021). Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain. Molecules and cells, 44(3), 179-185. https://doi.org/10.14348/molcells.2021.2235
Park, Sang-Sang, et al. "Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain." Molecules and cells vol. 44,3 (2021): 179-185. doi: https://doi.org/10.14348/molcells.2021.2235
Park SS, Lee S, Rhee DK. Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain. Mol Cells. 2021 Mar 31;44(3):179-185. doi: 10.14348/molcells.2021.2235. PMID: 33795535; PMCID: PMC8019601.
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Transcript structure and domain display: a customizable transcript visualization tool.

Bioinformatics (Oxford, England)

Watanabe KA, Ma K, Homayouni A, Rushton PJ, Shen QJ.
PMID: 27153680
Bioinformatics. 2016 Jul 01;32(13):2024-5. doi: 10.1093/bioinformatics/btw095. Epub 2016 Feb 22.

UNLABELLED: Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files...

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Watanabe KA, Ma K, Homayouni A, et al. Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics. 2016;32(13):2024-5doi: 10.1093/bioinformatics/btw095.
Watanabe, K. A., Ma, K., Homayouni, A., Rushton, P. J., & Shen, Q. J. (2016). Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics (Oxford, England), 32(13), 2024-5. https://doi.org/10.1093/bioinformatics/btw095
Watanabe, Kenneth A, et al. "Transcript structure and domain display: a customizable transcript visualization tool." Bioinformatics (Oxford, England) vol. 32,13 (2016): 2024-5. doi: https://doi.org/10.1093/bioinformatics/btw095
Watanabe KA, Ma K, Homayouni A, Rushton PJ, Shen QJ. Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics. 2016 Jul 01;32(13):2024-5. doi: 10.1093/bioinformatics/btw095. Epub 2016 Feb 22. PMID: 27153680.
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Crystal Structure of the PX Domain of SNX27.

Biochemistry. Biokhimiia

Li Y, Liao S, Li F, Zhu Z.
PMID: 31216973
Biochemistry (Mosc). 2019 Feb;84(2):147-152. doi: 10.1134/S0006297919020056.

SNX27 is a component of the retromer complex essential for the recycling of transmembrane receptors. SNX27 contains the N-terminal Phox (PX) domain that binds inositol 1,3-diphosphate (Ins(1,3)P

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Li Y, Liao S, Li F, et al. Crystal Structure of the PX Domain of SNX27. Biochemistry (Mosc). 2019;84(2):147-152doi: 10.1134/S0006297919020056.
Li, Y., Liao, S., Li, F., & Zhu, Z. (2019). Crystal Structure of the PX Domain of SNX27. Biochemistry. Biokhimiia, 84(2), 147-152. https://doi.org/10.1134/S0006297919020056
Li, Y, et al. "Crystal Structure of the PX Domain of SNX27." Biochemistry. Biokhimiia vol. 84,2 (2019): 147-152. doi: https://doi.org/10.1134/S0006297919020056
Li Y, Liao S, Li F, Zhu Z. Crystal Structure of the PX Domain of SNX27. Biochemistry (Mosc). 2019 Feb;84(2):147-152. doi: 10.1134/S0006297919020056. PMID: 31216973.
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Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA.

Structure (London, England : 1993)

Klein TA, Grebenc DW, Gandhi SY, Shah VS, Kim Y, Whitney JC.
PMID: 33238147
Structure. 2021 Feb 04;29(2):177-185.e6. doi: 10.1016/j.str.2020.11.002. Epub 2020 Nov 24.

Gram-positive bacteria use type VII secretion systems (T7SSs) to export effector proteins that manipulate the physiology of nearby prokaryotic and eukaryotic cells. Several mycobacterial T7SSs have established roles in virulence. By contrast, the genetically distinct T7SSb pathway found in...

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Klein TA, Grebenc DW, Gandhi SY, et al. Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA. Structure. 2020;29(2):177-185.e6doi: 10.1016/j.str.2020.11.002.
Klein, T. A., Grebenc, D. W., Gandhi, S. Y., Shah, V. S., Kim, Y., & Whitney, J. C. (2021). Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA. Structure (London, England : 1993), 29(2), 177-185.e6. https://doi.org/10.1016/j.str.2020.11.002
Klein, Timothy A, et al. "Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA." Structure (London, England : 1993) vol. 29,2 (2021): 177-185.e6. doi: https://doi.org/10.1016/j.str.2020.11.002
Klein TA, Grebenc DW, Gandhi SY, Shah VS, Kim Y, Whitney JC. Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA. Structure. 2021 Feb 04;29(2):177-185.e6. doi: 10.1016/j.str.2020.11.002. Epub 2020 Nov 24. PMID: 33238147.
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Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.

Frontiers in immunology

Ye Q, Lu S, Corbett KD.
PMID: 34381460
Front Immunol. 2021 Jul 26;12:719037. doi: 10.3389/fimmu.2021.719037. eCollection 2021.

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect...

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Ye Q, Lu S, Corbett KD. Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol. 2021;12:719037doi: 10.3389/fimmu.2021.719037.
Ye, Q., Lu, S., & Corbett, K. D. (2021). Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Frontiers in immunology, 12719037. https://doi.org/10.3389/fimmu.2021.719037
Ye, Qiaozhen, et al. "Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies." Frontiers in immunology vol. 12 (2021): 719037. doi: https://doi.org/10.3389/fimmu.2021.719037
Ye Q, Lu S, Corbett KD. Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol. 2021 Jul 26;12:719037. doi: 10.3389/fimmu.2021.719037. eCollection 2021. PMID: 34381460; PMCID: PMC8351461.
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Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif.

Communications biology

Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D.
PMID: 34316015
Commun Biol. 2021 Jul 27;4(1):916. doi: 10.1038/s42003-021-02387-5.

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal...

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Ultsch M, Holliday MJ, Gerhardy S, et al. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Commun Biol. 2021;4(1):916doi: 10.1038/s42003-021-02387-5.
Ultsch, M., Holliday, M. J., Gerhardy, S., Moran, P., Scales, S. J., Gupta, N., Oltrabella, F., Chiu, C., Fairbrother, W., Eigenbrot, C., & Kirchhofer, D. (2021). Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Communications biology, 4(1), 916. https://doi.org/10.1038/s42003-021-02387-5
Ultsch, Mark, et al. "Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif." Communications biology vol. 4,1 (2021): 916. doi: https://doi.org/10.1038/s42003-021-02387-5
Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Commun Biol. 2021 Jul 27;4(1):916. doi: 10.1038/s42003-021-02387-5. PMID: 34316015; PMCID: PMC8316464.
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How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation?.

Current opinion in structural biology

Borcherds W, Bremer A, Borgia MB, Mittag T.
PMID: 33069007
Curr Opin Struct Biol. 2021 Apr;67:41-50. doi: 10.1016/j.sbi.2020.09.004. Epub 2020 Oct 15.

Liquid-liquid phase separation is the mechanism underlying the formation of biomolecular condensates. Disordered protein regions often drive phase separation, but the molecular interactions mediating this phenomenon are not well understood, sometimes leading to the conflation that all disordered protein...

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Borcherds W, Bremer A, Borgia MB, et al. How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation?. Curr Opin Struct Biol. 2020;67:41-50doi: 10.1016/j.sbi.2020.09.004.
Borcherds, W., Bremer, A., Borgia, M. B., & Mittag, T. (2021). How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation?. Current opinion in structural biology, 6741-50. https://doi.org/10.1016/j.sbi.2020.09.004
Borcherds, Wade, et al. "How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation?." Current opinion in structural biology vol. 67 (2021): 41-50. doi: https://doi.org/10.1016/j.sbi.2020.09.004
Borcherds W, Bremer A, Borgia MB, Mittag T. How do intrinsically disordered protein regions encode a driving force for liquid-liquid phase separation?. Curr Opin Struct Biol. 2021 Apr;67:41-50. doi: 10.1016/j.sbi.2020.09.004. Epub 2020 Oct 15. PMID: 33069007; PMCID: PMC8044266.
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Showing 1 to 11 of 11 entries