6az2

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Crystal structure of Asf1-Fab 12E complex

Structural highlights

6az2 is a 6 chain structure with sequence from Baker's yeast and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:ASF1, CIA1, YJL115W, J0755 (Baker's yeast)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ASF1_YEAST] Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly. Facilitates histone deposition through both replication-dependent and replication-independent chromatin assembly pathways. Cooperates with chromatin assembly factor 1 (CAF-1) to promote replication-dependent chromatin assembly and with the HIR complex to promote replication-independent chromatin assembly, which may occur during transcription and DNA repair. May be required for the maintenance of a subset of replication elongation factors, including DNA polymerase epsilon, the RFC complex and PCNA, at stalled replication forks. Also required for acetylation of histone H3 on 'Lys-9' and 'Lys-56'.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]

Publication Abstract from PubMed

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.,Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA J Mol Biol. 2017 Dec 19. pii: S0022-2836(17)30593-4. doi:, 10.1016/j.jmb.2017.12.012. PMID:29273204[40]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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References

  1. ↑ Le S, Davis C, Konopka JB, Sternglanz R. Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast. 1997 Sep 15;13(11):1029-42. PMID:9290207 doi:<1029::AID-YEA160>3.0.CO;2-1 http://dx.doi.org/10.1002/(SICI)1097-0061(19970915)13:11<1029::AID-YEA160>3.0.CO;2-1
  2. ↑ Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 1999 Dec 2;402(6761):555-60. PMID:10591219 doi:http://dx.doi.org/10.1038/990147
  3. ↑ Sharp JA, Fouts ET, Krawitz DC, Kaufman PD. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr Biol. 2001 Apr 3;11(7):463-73. PMID:11412995
  4. ↑ Hu F, Alcasabas AA, Elledge SJ. Asf1 links Rad53 to control of chromatin assembly. Genes Dev. 2001 May 1;15(9):1061-6. PMID:11331602 doi:http://dx.doi.org/10.1101/gad.873201
  5. ↑ Osada S, Sutton A, Muster N, Brown CE, Yates JR 3rd, Sternglanz R, Workman JL. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 2001 Dec 1;15(23):3155-68. PMID:11731479 doi:http://dx.doi.org/10.1101/gad.907201
  6. ↑ Meijsing SH, Ehrenhofer-Murray AE. The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 2001 Dec 1;15(23):3169-82. PMID:11731480 doi:http://dx.doi.org/10.1101/gad.929001
  7. ↑ Sutton A, Bucaria J, Osley MA, Sternglanz R. Yeast ASF1 protein is required for cell cycle regulation of histone gene transcription. Genetics. 2001 Jun;158(2):587-96. PMID:11404324
  8. ↑ Emili A, Schieltz DM, Yates JR 3rd, Hartwell LH. Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1. Mol Cell. 2001 Jan;7(1):13-20. PMID:11172707
  9. ↑ Umehara T, Chimura T, Ichikawa N, Horikoshi M. Polyanionic stretch-deleted histone chaperone cia1/Asf1p is functional both in vivo and in vitro. Genes Cells. 2002 Jan;7(1):59-73. PMID:11856374
  10. ↑ Krawitz DC, Kama T, Kaufman PD. Chromatin assembly factor I mutants defective for PCNA binding require Asf1/Hir proteins for silencing. Mol Cell Biol. 2002 Jan;22(2):614-25. PMID:11756556
  11. ↑ Chimura T, Kuzuhara T, Horikoshi M. Identification and characterization of CIA/ASF1 as an interactor of bromodomains associated with TFIID. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9334-9. Epub 2002 Jul 1. PMID:12093919 doi:http://dx.doi.org/10.1073/pnas.142627899
  12. ↑ Robinson KM, Schultz MC. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol Cell Biol. 2003 Nov;23(22):7937-46. PMID:14585955
  13. ↑ Prado F, Cortes-Ledesma F, Aguilera A. The absence of the yeast chromatin assembly factor Asf1 increases genomic instability and sister chromatid exchange. EMBO Rep. 2004 May;5(5):497-502. Epub 2004 Apr 8. PMID:15071494 doi:http://dx.doi.org/10.1038/sj.embor.7400128
  14. ↑ Adkins MW, Tyler JK. The histone chaperone Asf1p mediates global chromatin disassembly in vivo. J Biol Chem. 2004 Dec 10;279(50):52069-74. Epub 2004 Sep 26. PMID:15452122 doi:http://dx.doi.org/10.1074/jbc.M406113200
  15. ↑ Adkins MW, Howar SR, Tyler JK. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell. 2004 Jun 4;14(5):657-66. PMID:15175160 doi:http://dx.doi.org/10.1016/j.molcel.2004.05.016
  16. ↑ Glowczewski L, Waterborg JH, Berman JG. Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol Cell Biol. 2004 Dec;24(23):10180-92. PMID:15542829 doi:http://dx.doi.org/10.1128/MCB.24.23.10180-10192.2004
  17. ↑ Ramey CJ, Howar S, Adkins M, Linger J, Spicer J, Tyler JK. Activation of the DNA damage checkpoint in yeast lacking the histone chaperone anti-silencing function 1. Mol Cell Biol. 2004 Dec;24(23):10313-27. PMID:15542840 doi:http://dx.doi.org/10.1128/MCB.24.23.10313-10327.2004
  18. ↑ Robinson KM, Schultz MC. Gal4-VP16 directs ATP-independent chromatin reorganization in a yeast chromatin assembly system. Biochemistry. 2005 Mar 22;44(11):4551-61. PMID:15766286 doi:http://dx.doi.org/10.1021/bi047523u
  19. ↑ Green EM, Antczak AJ, Bailey AO, Franco AA, Wu KJ, Yates JR 3rd, Kaufman PD. Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol. 2005 Nov 22;15(22):2044-9. PMID:16303565 doi:http://dx.doi.org/S0960-9822(05)01306-0
  20. ↑ Harkness TA, Arnason TG, Legrand C, Pisclevich MG, Davies GF, Turner EL. Contribution of CAF-I to anaphase-promoting-complex-mediated mitotic chromatin assembly in Saccharomyces cerevisiae. Eukaryot Cell. 2005 Apr;4(4):673-84. PMID:15821127 doi:http://dx.doi.org/4/4/673
  21. ↑ Franco AA, Lam WM, Burgers PM, Kaufman PD. Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes Dev. 2005 Jun 1;19(11):1365-75. Epub 2005 May 18. PMID:15901673 doi:http://dx.doi.org/10.1101/gad.1305005
  22. ↑ Sharp JA, Rizki G, Kaufman PD. Regulation of histone deposition proteins Asf1/Hir1 by multiple DNA damage checkpoint kinases in Saccharomyces cerevisiae. Genetics. 2005 Nov;171(3):885-99. Epub 2005 Jul 14. PMID:16020781 doi:http://dx.doi.org/10.1534/genetics.105.044719
  23. ↑ Linger J, Tyler JK. The yeast histone chaperone chromatin assembly factor 1 protects against double-strand DNA-damaging agents. Genetics. 2005 Dec;171(4):1513-22. Epub 2005 Sep 2. PMID:16143623 doi:http://dx.doi.org/genetics.105.043000
  24. ↑ Schermer UJ, Korber P, Horz W. Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Mol Cell. 2005 Jul 22;19(2):279-85. PMID:16039596 doi:http://dx.doi.org/10.1016/j.molcel.2005.05.028
  25. ↑ Zabaronick SR, Tyler JK. The histone chaperone anti-silencing function 1 is a global regulator of transcription independent of passage through S phase. Mol Cell Biol. 2005 Jan;25(2):652-60. PMID:15632066 doi:http://dx.doi.org/25/2/652
  26. ↑ Osada S, Kurita M, Nishikawa J, Nishihara T. Chromatin assembly factor Asf1p-dependent occupancy of the SAS histone acetyltransferase complex at the silent mating-type locus HMLalpha. Nucleic Acids Res. 2005 May 12;33(8):2742-50. Print 2005. PMID:15891116 doi:http://dx.doi.org/33/8/2742
  27. ↑ Lewis LK, Karthikeyan G, Cassiano J, Resnick MA. Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair. Nucleic Acids Res. 2005 Sep 1;33(15):4928-39. Print 2005. PMID:16141196 doi:http://dx.doi.org/33/15/4928
  28. ↑ Mousson F, Lautrette A, Thuret JY, Agez M, Courbeyrette R, Amigues B, Becker E, Neumann JM, Guerois R, Mann C, Ochsenbein F. Structural basis for the interaction of Asf1 with histone H3 and its functional implications. Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):5975-80. Epub 2005 Apr 19. PMID:15840725
  29. ↑ Celic I, Masumoto H, Griffith WP, Meluh P, Cotter RJ, Boeke JD, Verreault A. The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. Curr Biol. 2006 Jul 11;16(13):1280-9. PMID:16815704 doi:http://dx.doi.org/S0960-9822(06)01749-0
  30. ↑ Linger J, Tyler JK. Global replication-independent histone H4 exchange in budding yeast. Eukaryot Cell. 2006 Oct;5(10):1780-7. Epub 2006 Aug 25. PMID:16936140 doi:http://dx.doi.org/10.1128/EC.00202-06
  31. ↑ Tamburini BA, Carson JJ, Linger JG, Tyler JK. Dominant mutants of the Saccharomyces cerevisiae ASF1 histone chaperone bypass the need for CAF-1 in transcriptional silencing by altering histone and Sir protein recruitment. Genetics. 2006 Jun;173(2):599-610. Epub 2006 Apr 2. PMID:16582440 doi:http://dx.doi.org/10.1534/genetics.105.054783
  32. ↑ Korber P, Barbaric S, Luckenbach T, Schmid A, Schermer UJ, Blaschke D, Horz W. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J Biol Chem. 2006 Mar 3;281(9):5539-45. Epub 2006 Jan 4. PMID:16407267 doi:http://dx.doi.org/M513340200
  33. ↑ Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem. 2006 Dec 8;281(49):37270-4. Epub 2006 Oct 17. PMID:17046836 doi:http://dx.doi.org/10.1074/jbc.C600265200
  34. ↑ Schwabish MA, Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol Cell. 2006 May 5;22(3):415-22. PMID:16678113 doi:http://dx.doi.org/S1097-2765(06)00180-8
  35. ↑ Kats ES, Albuquerque CP, Zhou H, Kolodner RD. Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants. Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3710-5. Epub 2006 Feb 24. PMID:16501045 doi:http://dx.doi.org/0511102103
  36. ↑ Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6988-93. Epub 2006 Apr 20. PMID:16627621 doi:http://dx.doi.org/0601676103
  37. ↑ Adkins MW, Carson JJ, English CM, Ramey CJ, Tyler JK. The histone chaperone anti-silencing function 1 stimulates the acetylation of newly synthesized histone H3 in S-phase. J Biol Chem. 2007 Jan 12;282(2):1334-40. Epub 2006 Nov 15. PMID:17107956 doi:http://dx.doi.org/M608025200
  38. ↑ Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X
  39. ↑ Daganzo SM, Erzberger JP, Lam WM, Skordalakes E, Zhang R, Franco AA, Brill SJ, Adams PD, Berger JM, Kaufman PD. Structure and function of the conserved core of histone deposition protein Asf1. Curr Biol. 2003 Dec 16;13(24):2148-58. PMID:14680630
  40. ↑ Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J Mol Biol. 2017 Dec 19. pii: S0022-2836(17)30593-4. doi:, 10.1016/j.jmb.2017.12.012. PMID:29273204 doi:http://dx.doi.org/10.1016/j.jmb.2017.12.012

Contents


6az2, resolution 2.48Å

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