Abstract
This chapter will first introduce you to the freely accessible data bank of protein structures (the “PDB”) and show you how to search, access, and understand the information within it. The second half presents a tool, PyMOL, with which you can start to visualize and analyze the data stored in the PDB.
We are now living in an atomic age. In order to understand the world, every person needs to have some understanding of atoms and molecules. Linus Pauling and Roger Hayward (Pauling and Hayward 1964)
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References
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213–221. https://doi.org/10.1107/S0907444909052925
Alber T, Sun DP, Wilson K, Wozniak JA, Cook SP, Matthews BW (1987) Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme. Nature 330(6143):41–46. https://doi.org/10.1038/330041a0
Anon (1971) Protein Data Bank. Nat New Biol 233(42):223
Aumayr M, Schrempf A, Uzulmez O, Olek KM, Skern T (2017) Interaction of 2A proteinase of human rhinovirus genetic group A with eIF4E is required for eIF4G cleavage during infection. Virology 511:123–134. https://doi.org/10.1016/j.virol.2017.08.020
Baase WA, Liu L, Tronrud DE, Matthews BW (2010) Lessons from the lysozyme of phage T4. Protein Sci 19(4):631–641. https://doi.org/10.1002/pro.344
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235–242
Berman HM, Kleywegt GJ, Nakamura H, Markley JL (2012) The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure 20(3):391–396. https://doi.org/10.1016/j.str.2012.01.010
Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280(5360):69–77
Drenth J, Kalk KH, Swen HM (1976) Binding of chloromethyl ketone substrate analogues to crystalline papain. Biochemistry 15(17):3731–3738
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of coot. Acta Crystallogr D Biol Crystallogr 66(Pt 4):486–501. https://doi.org/10.1107/S0907444910007493
Goldstone DC, Walker PA, Calder LJ, Coombs PJ, Kirkpatrick J, Ball NJ, Hilditch L, Yap MW, Rosenthal PB, Stoye JP, Taylor IA (2014) Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice. Proc Natl Acad Sci U S A 111(26):9609–9614. https://doi.org/10.1073/pnas.1402448111
Goodsell DS, Dutta S, Zardecki C, Voigt M, Berman HM, Burley SK (2015) The RCSB PDB “Molecule of the month”: inspiring a molecular view of biology. PLoS Biol 13(5):e1002140. https://doi.org/10.1371/journal.pbio.1002140
Holm L, Laakso LM (2016) Dali server update. Nucleic Acids Res 44(W1):W351–W355. https://doi.org/10.1093/nar/gkw357
Kamphuis IG, Kalk KH, Swarte MB, Drenth J (1984) Structure of papain refined at 1.65 Å resolution. J Mol Biol 179(2):233–256
Matthews BW, Remington SJ (1974) The three dimensional structure of the lysozyme from bacteriophage T4. Proc Natl Acad Sci U S A 71(10):4178–4182
Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L, Selk L, Kent SB, Wlodawer A (1989) Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science 246(4934):1149–1152
Pauling L, Hayward R (1964) The architecture of molecules. WH Freeman, San Francisco
Rose PW, Prlic A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45(D1):D271–D281. https://doi.org/10.1093/nar/gkw1000
Schwartz TW, Sakmar TP (2011) Structural biology: snapshot of a signalling complex. Nature 477(7366):540–541. https://doi.org/10.1038/477540a
Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64(Pt 1):112–122. https://doi.org/10.1107/S0108767307043930
The PyMOL Molecular Graphics System, Schrödinger, LLC
Weaver LH, Matthews BW (1987) Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution. J Mol Biol 193(1):189–199
Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB (1989) Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 245(4918):616–621
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Skern, T. (2018). An Archive and a Tool: PDB and PyMOL. In: Exploring Protein Structure: Principles and Practice. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-319-76858-8_2
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DOI: https://doi.org/10.1007/978-3-319-76858-8_2
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