Structure of the human NF-κB p52 homodimer-DNA complex at 2.1 A resolution

EMBO Journal

Volumn 16, Issue 23, 1997, Pages 7078-7090

  Cramer, Patrick ^a   Larson, Christopher J ^b,c   Verdine, Gregory L ^b   Müller, Christoph W ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (France)

^b HARVARD UNIVERSITY   (United States)

^c SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

Crystal structure; NF B p52; Protein DNA interaction; Rel protein; Transcription

Indexed keywords

CELL PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PROTEIN P52; TRANSCRIPTION FACTOR REL; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA PROTEIN COMPLEX; PRIORITY JOURNAL; PROTEIN DNA BINDING; STEREOCHEMISTRY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NF-KAPPA B; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-REL; SEQUENCE HOMOLOGY, AMINO ACID; WATER;

EID: 0030723630     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Baeuerle, P.A. and Baltimore, D. (1996) NF-κB: ten years after. Cell, 87, 13-20.
2. Baeuerle, P.A. and Henkel, T. (1994) Function and activation of NF-κB in the immune system. Annu. Rev. Immunol., 12, 141-179.
3. Baldwin, A. (1996) The NF-κB and IκB proteins: new discoveries and insights. Annu. Rev. Immunol., 14, 649-681.
4. Baldwin, A., Jr and Sharp, P.A. (1987) Binding of a nuclear factor to a regulatory sequence in the promoter of the mouse H-2 κB class I major histocompatibility gene. Mol. Cell. Biol., 7, 305-313.
5. Baldwin, A., Jr and Sharp, P.A. (1988) Two transcription factors, NF-κB and H2TF1, interact with a single regulatory sequence in the class I major histocompatibility complex promoter. Proc. Natl Acad. Sci. USA, 85, 723-727.
6. Barillas-Mury, C., Charlesworth, A., Gross, I., Richman, A., Hoffmann, J.A. and Kafatos, F.C. (1996) Immune factor Gambif1, a new rel family member from the human malaria vector, Anopheles gambiae. EMBO J., 15, 4691-4701.
7. Bass, S., Sorrells, V. and Youderian, P. (1988) Mutant Trp repressors with new DNA binding specificities. Science, 242, 240-245.
8. Berman, H.M. (1991) Hydration of DNA. Curr. Opin. Struct. Biol., 1, 423-427.
9. Berman, H.M. (1994) Hydration of DNA: take 2. Curr. Opin. Struct. Biol., 4, 345-350.
10. Blackburn, G.M. and Gait, M.J. (1996) Nucleic Acids in Chemistry and Biology. Oxford University Press, Oxford, UK.
11. Bours, V., Franzoso, G., Azarenko, V., Park, S., Kanno, T., Brown, K. and Siebenlist, U. (1993) The oncoprotein Bcl-3 directly transactivates through κB motifs via association with DNA binding p50B homodimers. Cell, 72, 729-739.
12. Brünger, A.T. (1992) X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
13. CCP4 (1994) Collaborative Computational Project Number 4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr., D50, 760-776.
14. Chang, C.C., Zhang, J., Lombardi, L., Neri, A. and Dalla-Favera, R. (1994) Mechanism of expression and role in transcriptional control of the proto-oncogene NFKB-2/LYT-10. Oncogene, 9, 923-933.
15. Chytil, M. and Verdine, G.L. (1996) The Rel family of eukaryotic transcription factors. Curr. Opin. Struct. Biol., 6, 91-100.
16. Cramer, P. and Müller, C.W. (1997) Engineering of diffraction-quality crystals of the NF-κB p52 homodimer-DNA complex. FEBS Lett., 405, 373-377.
17. Dickerson, R.E., Goodsell, D.S. and Neidle, S. (1994) '...the tyranny of the lattice...'. Proc. Natl Acad. Sci. USA, 91, 3579-3583.
18. Duckett, C.S., Perkins, N.D., Kowalik, T.F., Schmid, R.M., Huang, E.S., Baldwin, A., Jr and Nabel, G.J. (1993) Dimerization of NF-κB2 with RelA(p65) regulates DNA binding, transcriptional activation, and inhibition by an IκB-α (MAD-3). Mol. Cell. Biol., 13, 1315-1322.
19. Franzoso, G., Bours, V., Azarenko, V., Park, S., Tomita-Yamaguchi, M., Kanno, T., Brown, K. and Siebenlist, U. (1993) The oncoprotein Bcl-3 can facilitate NF-κB-mediated transactivation by removing inhibiting p50 homodimers from select κB sites. EMBO J., 12, 3893-3901.
20. Ghosh, G., van Duyne, G., Ghosh, S. and Sigler, P.B. (1995) Structure of NF-κB p50 homodimer bound to a κB site. Nature, 373, 303-310.
21. Gilmore, T.D. and Morin, P.J. (1993) The IκB proteins: members of a multifunctional family. Trends Genet., 9, 427-433.
22. Gutsch, D.E., Holley-Guthrie, E.A., Zhang, Q., Stein, B., Blanar, M.A., Baldwin, A.S. and Kenney, S.C. (1994) The bZIP transactivator of Epstein-Barr virus, BZLF1, functionally and physically interacts with the p65 subunit of NF-κB. Mol. Cell. Biol., 14, 1939-1948.
23. Hassan, M.A.E. and Calladine, C.R. (1996) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol., 259, 95-103.
24. Joachimiak, A., Haran, T.E. and Sigler, P.B. (1994) Mutagenesis supports water mediated recognition in the trp repressor-operator system. EMBO J., 13, 367-372.
25. Jones, A.T., Zhou, J.-Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, 110-119.
26. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
27. Kumar, S., Rabson, A.B. and Gelinas, C. (1992) The RxxRxRxxC motif conserved in all Rel/κB proteins is essential for the DNA binding activity and redox regulation of the v-Rel oncoprotein. Mol. Cell. Biol., 12, 3094-3106.
28. Labeots, L.A. and Weiss, M.A. (1997) Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity. J. Mol. Biol., 269, 113-128.
29. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
30. Lavery, R. and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam., 6, 63-91.
31. Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
32. Lin, R., Gewert, D. and Hiscott, J. (1995) Differential transcriptional activation in vitro by NF-κB/Rel proteins. J. Biol. Chem., 270, 3123-3131.
33. Matthews, B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
34. Merritt, E.A. and Murphy, M.E.P. (1994) Raster3D Version 2.0-a program for photorealistic molecular graphics. Acta Crystallogr., D50, 869-873.
35. Müller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L. and Harrison, S.C. (1995) Structure of the NF-κB p50 homodimer bound to DNA. Nature, 373, 311-317.
36. Müller, C.W., Rey, F.A. and Harrison, S.C. (1996) Comparison of two different DNA-binding modes of the NF-κB p50 homodimer. Nature Struct. Biol., 3, 224-227.
37. Navaza, J. (1994) AMoRe: an automated program package for molecular replacement. Acta Crystallogr., A50, 157-163.
38. Nolan, G.P. (1994) NF-AT-AP-1 and Rel-bZIP: hybrid vigor and binding under the influence. Cell, 77, 795-798.
39. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
40. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A.T. and Berman, H.M. (1996) New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr., D52, 57-64.
41. Perkins, N.D., Schmid, R.M., Duckett, C.S., Leung, K., Rice, N.R. and Nabel, G.J. (1992) Distinct combinations of NF-κB subunits determine the specificity of transcriptional activation. Proc. Natl Acad. Sci. USA, 89, 1529-1533.
42. Peterson, B.R., Sun, L.J. and Verdine, G.L. (1996) A critical arginine residue mediates cooperativity in the contact interface between transcription factors NFAT and AP-1. Proc. Natl Acad. Sci. USA, 93, 13671-13676.
43. Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
44. Rost, B. (1996) PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol., 266, 525-539.
45. Schmid, R.M., Perkins, N.D., Duckett, C.S., Andrews, P.C. and Nabel, G.J. (1991) Cloning of an NF-κB subunit which stimulates HIV transcription in synergy with p65. Nature, 352, 733-736.
46. Schmid, R.M., Liptay, S., Betts, J.C. and Nabel, G.J. (1994) Structural and functional analysis of NF-κB. Determinants of DNA binding specificity and protein interaction. J. Biol. Chem., 269, 32162-32167.
47. Schwabe, J.W. (1997) The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol., 7, 126-134.
48. Stein, B. and Baldwin, A., Jr (1993) Distinct mechanisms for regulation of the interleukin-8 gene involve synergism and cooperativity between C/EBP and NF-κB. Mol. Cell. Biol., 13, 7191-7198.
49. Stein, B., Baldwin, A., Jr. Ballard, D.W., Greene, W.C., Angel, P. and Herrlich, P. (1993a) Cross-coupling of the NF-κB p65 and Fos/ Jun transcription factors produces potentiated biological function. EMBO J., 12, 3879-3891.
50. Stein, B., Cogswell, P.C. and Baldwin, A., Jr (1993b) Functional and physical associations between NF-κB and C/EBP family members: a Rel domain-bZIP interaction. Mol. Cell. Biol., 13, 3964-3974.
51. Thanos, D. and Maniatis, T. (1992) The high mobility group protein HMG I(Y) is required for NF-κB-dependent virus induction of the human IFN-β gene. Cell, 71, 777-789.
52. Thanos, D. and Maniatis, T. (1995) NF-κB: a lesson in family values. Cell, 80, 529-532.
53. Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graph., 8, 52-56.
54. Wilson, D.S., Guenther, B., Desplan, C. and Kuriyan, J. (1995) High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell, 82, 709-719.
55. Wolfe, S.A., Zhou, P., Dotsch, V., Chen, L., You, A., Ho, S.N., Crabtree, G.R., Wagner, G. and Verdine, G.L. (1997) Unusual Rel-like architecture in the DNA binding domain of the transcription factor NFATc. Nature, 385, 172-176.