The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Correction of the NMR structure of the ETS1/DNA complex
Abstract
The ETS family of transcription factors consists of a group of proteins that share a highly conserved 85 amino acid DNA-binding domain (DBD). This family recognizes a consensus sequence rich in purine bases with a central GGAA motif. A comparison of the published three-dimensional structures of the DBD/DNA complexes of ETS1 by NMR [Werner et al. (1995) Cell, 83, 761-771] and the related Pu.1 by X-ray crystallography [Kodandapani et al. (1996) Nature, 380, 456-460] reveals an apparent discrepancy in which the protein domains bind with opposite polarity to their target sequences. This surprising and highly unlikely result prompted us to reexamine our NMR structure. Additional NMR experiments now reveal an error in the original interpretation of the spectra defining the orientation of the ETS1-DBD on DNA. It was originally reported that the ETS1-DBD bound to DNA with a bipartite motif involving major groove recognition via a helix-turn-helix element and minor groove recognition via protein side-chain intercalation. The presence of intercalation was deduced on the basis of numerous NOEs between several amino acids in the protein and a resonance at 12.33 ppm originally assigned to a DNA imino proton. New NMR experiments now conclusively demonstrate that this resonance, which is located within the DNA imino proton region of the spectrum, arises from the hydroxyl proton of Tyr86. Realization of this error necessitated reanalysis of the intermolecular NOEs. This revealed that the orientation of the ETS1-DBD in the complex is opposite to that originally reported and that a tryptophan residue does not intercalate into the DNA. The calculation of a new ensemble of structures based on the corrected data indicates that the structure of the ETS1-DBD/DNA complex is indeed similar to the X-ray structure of the Pu.1-DBD/DNA complex.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The overall structure and DNA-binding mechanism of the ETS domain is based on high-resolution molecular models of ten family members from X-ray crystallography and NMR.
“The overall structure and DNA-binding mechanism of the ETS domain is based on high-resolution molecular models of ten family members derived from both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy (Figure 1b, Supplemental Table 2) (37–51).”
From Genomic and biochemical insights into the specificity of ETS transcription factors (2011) · cites this paper as [39]
Citations
Cites
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., & Bax, A. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197809 · Cited by 15,961
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
Nicholls, A. O., Sharp, K. A., & Honig, B. H. (1991) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340110407 · Cited by 5,230
Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences
Plateau, P., & Guéron, M. (1982) · Journal of the American Chemical Society · doi:10.1021/ja00389a067 · Cited by 1,062
The Ets family of transcription factors
Wasylyk, B., Hahn, S. L., & Giovane, A. (1993) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1993.tb19864.x · Cited by 839
Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn
Rice, P. A., Yang, S., Mizuuchi, K., & Nash, H. A. (1996) · Cell · doi:10.1016/s0092-8674(00)81824-3 · Cited by 819
Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer
Lewis, M., Chang, G. A., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G., & Lu, P. (1996) · Science · doi:10.1126/science.271.5253.1247 · Cited by 790
Garrett, D. S., Powers, R., Gronenborn, A. M., & Clore, G. M. (1991) · Journal of Magnetic Resonance (1969) · doi:10.1016/0022-2364(91)90341-p · Cited by 682
Self-citationStructural basis for DNA bending by the architectural transcription factor LEF-1
Love, J. J., Li, X., Case, D. A., Giese, K., Grosschedl, R., & Wright, P. E. (1995) · Nature · doi:10.1038/376791a0 · Cited by 573
Nilges, M., Clore, G. M., & Gronenborn, A. M. (1988) · FEBS Letters · doi:10.1016/0014-5793(88)80559-3 · Cited by 542
Self-citationKraulis, P. J., Clore, G. M., Nilges, M., Jones, T. A., Pettersson, G., Knowles, J., & Gronenborn, A. M. (1989) · Biochemistry · doi:10.1021/bi00444a016 · Cited by 512
Self-citationWerner, M. H., Huth, J. R., Gronenborn, A. M., & Clore, G. M. (1995) · Cell · doi:10.1016/0092-8674(95)90532-4 · Cited by 464
Self-citationNye, J. A., Petersen, J. M., Gunther, C. V., Jonsen, M. D., & Graves, B. J. (1992) · Genes & Development · doi:10.1101/gad.6.6.975 · Cited by 363
A new pattern for helix–turn–helix recognition revealed by the PU.l ETS–domain–DNA complex
Kodandapani, R., Pio, F., Ni, C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R. A., & Ely, K. R. (1996) · Nature · doi:10.1038/380456a0 · Cited by 315 · cited 16×
“…DBD structures of mouse ETS1 (Donaldson et al., 1994,1996), human Fli-1 (Liang et al., 1994a,b), human ETS1 (Werner et al., 1995b) and mouse Pu.1 (Kodandapani et al., 1996) reveal an overall fold that is very similar to that of the DBD of the E. coli catabolite gene activator protein (CAP),…”
BackgroundMethodInfluentialA calculation strategy for the structure determination of symmetric demers by 1H NMR
Nilges, M. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170307 · Cited by 308
Macleod, K., Leprince, D., & Stehelin, D. (1992) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(92)90404-w · Cited by 304
Intercalation, DNA Kinking, and the Control of Transcription
Werner, M. H., Gronenborn, A. M., & Clore, G. M. (1996) · Science · doi:10.1126/science.271.5250.778 · Cited by 280
Self-citationKuszewski, J. J., Qin, J., Gronenborn, A. M., & Clore, G. M. (1995) · Journal of Magnetic Resonance Series B · doi:10.1006/jmrb.1995.1017 · Cited by 208
Self-citationModulation of Transcription Factor Ets-1 DNA Binding: DNA-Induced Unfolding of an α Helix
Petersen, J. M., Skalicky, J. J., Donaldson, L. W., McIntosh, L. P., Alber, T., & Graves, B. J. (1995) · Science · doi:10.1126/science.7569926 · Cited by 176
Solution structure of the ETS domain from murine Ets‐1: a winged helix‐turn‐helix DNA binding motif.
Donaldson, L. W., Petersen, J. M., Graves, B. J., & McIntosh, L. P. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00340.x · Cited by 159
Inhibition of hematopoiesis by competitive binding of transcription factor PU.1
Voso, M. T., Burn, T. C., Wulf, G., Lim, B., Leone, G., & Tenen, D. G. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.17.7932 · Cited by 141
King, C., & Weiss, M. A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.24.11990 · Cited by 138
Garrett, D. S., Kuszewski, J. J., Hancock, T. J., Lodi, P. J., Vuister, G. W., Gronenborn, A. M., & Clore, G. M. (1994) · Journal of Magnetic Resonance Series B · doi:10.1006/jmrb.1994.1061 · Cited by 136
Self-citationStaphylococcal nuclease: sequential assignments and solution structure
Torchia, D. A., Sparks, S. W., & Bax, A. (1989) · Biochemistry · doi:10.1021/bi00439a028 · Cited by 133
Fisher, R. J., Fivash, M. J., Casas‐Finet, J. R., Erickson, J. W., Kondoh, A., Bladen, S. V., Fisher, C. L., Watson, D. K., & Papas, T. S. (1994) · Protein Science · doi:10.1002/pro.5560030210 · Cited by 127
Self-citationNMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins
Liepinsh, E., Otting, G., & Wüthrich, K. (1992) · Journal of Biomolecular NMR · doi:10.1007/bf02192808 · Cited by 123
Zhao, Q., Abeygunawardana, C., Talalay, P., et al. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8220 · Cited by 115
Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L. B., Shiloach, J., & Gronenborn, A. M. (1995) · Cell · doi:10.1016/0092-8674(95)90189-2 · Cited by 109
Self-citationRefolding proteins by gel filtration chromatography
Werner, M. H., Clore, G. M., Gronenborn, A. M., Kondoh, A., & Fisher, R. J. (1994) · FEBS Letters · doi:10.1016/0014-5793(94)00401-3 · Cited by 108
Self-citationRay-Gallet, D., Mao, C. D., Tavitian, A., & Moreau-Gachelin, F. (1995) · PubMed · Cited by 105
Solution structure of the ets domain of Fli-1 when bound to DNA
Liang, H., Mao, X., Olejniczak, E. T., Nettesheim, D. G., Yu, L., Meadows, R. P., Thompson, C. B., & Fesik, S. W. (1994) · Nature Structural & Molecular Biology · doi:10.1038/nsb1294-871 · Cited by 104
Blake, P. R., Lee, B., Summers, M. F., et al. (1992) · Journal of Biomolecular NMR · doi:10.1007/bf02192814 · Cited by 94
Assignment of the backbone proton and nitrogen-15 NMR resonances of bacteriophage T4 lysozyme
McIntosh, L. P., Wand, A. J., Lowry, D. F., et al. (1990) · Biochemistry · doi:10.1021/bi00479a003 · Cited by 85
The ETS-domain transcription factors Elk-1 and SAP-1 exhibit differential DNA binding specifitoies
Shore, P., & Sharrocks, A. D. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.22.4698 · Cited by 83
Donaldson, L. W., Petersen, J. M., Graves, B. J., & McIntosh, L. P. (1994) · Biochemistry · doi:10.1021/bi00250a001 · Cited by 81
Fisher, R. J., Mavrothalassitis, G., Kondoh, A., & Papas, T. S. (1991) · PubMed · Cited by 79
Self-citationStructures of Protein Complexes by Multidimensional Heteronuclear Magnetic Resonance Spectroscopy
Gronenborn, A. M., & Clore, G. M. (1995) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239509083489 · Cited by 77
Self-citationGalson, D. L., & Housman, D. E. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.1.381-392.1988 · Cited by 65
Plesniak, L. A., Connelly, G. P., McIntosh, L. P., & Wakarchuk, W. W. (1996) · Protein Science · doi:10.1002/pro.5560051118 · Cited by 63
Werner, M. H., Bianchi, M. E., Gronenborn, A. M., et al. (1995) · Biochemistry · doi:10.1021/bi00037a042 · Cited by 60
Self-citationThe ETS oncogene family in development, proliferation and neoplasia.
Hromas, R., & Klemsz, M. (1994) · PubMed · Cited by 54
Liang, H., Olejniczak, E. T., Mao, X., Nettesheim, D. G., Yu, L. P., Thompson, C. B., & Fesik, S. W. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.24.11655 · Cited by 49
Galson, D. L., Hensold, J. O., Bishop, T. R., Schalling, M., D'Andrea, A. D., Jones, C., Auron, P. E., & Housman, D. E. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.5.2929-2941.1993 · Cited by 45
Graves, B. J., Gillespie, M. E., & Mclntosh, L. P. (1996) · Nature · doi:10.1038/384322a0 · Cited by 28
Pjura, P. E., McIntosh, L. P., Wozniak, J. A., & Matthews, B. W. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340150407 · Cited by 17
Werner, M. H., Clore, G. M., Fisher, C. L., et al. (1996) · Cell · doi:10.1016/s0092-8674(00)81354-9 · Cited by 10
Self-citation
Flagged first, then by citations
Research works printed but not linked: 8
- Brünger, A.T. (1993) XPLOR Manual Version 3.1, Yale University, New Haven, CT, U.S.A.
- Fisher, R.J., Mavrothalassitis, G., Kondoh, A. and Papas, T.S. (1991) Oncogene, 6, 2249–2254.
- Galson, D.L. and Housman, D.E. (1988) Mol.Cell.Biol., 8, 381–392.
- Galson, D.L., Hensold, J.O., Bishop, T.R., Schalling, M., D'Andrea, A.D., Jones, C., Auron, P.E. and Housman, D.E. (1993) Mol.Cell. Biol., 13, 2929–2941.
- Garrett, D.S., Powers, R., Gronenborn, A.M. and Clore, G.M. (1991) J.Magn.Reson., 95, 214–220.
- Hromas, R. and Klemsz, M. (1994) Int.J.Hematol., 59, 257–265.
- Morris, A.L., MacArthur, M.W., Hutchinson, E.G. and Thornton, A.M. (1992) Proteins Struct.Funct.Genet., 78, 1595–1620.
- Ray-Gallet, D., Mao, C., Tavitian, A. and Moreau-Gachelin, F. (1995) Oncogene, 11, 303–313.
Cited by
Sorted by citations
The mutational landscape of lethal castration-resistant prostate cancer
Grasso, C. S., Wu, Y.-M., Robinson, D. R., Cao, X., Dhanasekaran, S. M., Khan, A. P., Quist, M. J., Jing, X., Lonigro, R. J., Brenner, J. C., et al. (2012) · Nature · doi:10.1038/nature11125 · Cited by 2,517
The ETS-domain transcription factor family
Sharrocks, A. D. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35099076 · Cited by 1,086
Genomic and biochemical insights into the specificity of ETS transcription factors
Hollenhorst, P. C., McIntosh, L. P., & Graves, B. J. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.79.081507.103945 · Cited by 490
Specificity within the ets Family of Transcription Factors
(1998) · Advances in Cancer Research · doi:10.1016/s0065-230x(08)60738-1 · Cited by 344
Phosphorylation represses Ets-1 DNA binding by reinforcing autoinhibition
Cowley, D. O., & Graves, B. J. (2000) · Genes & Development · doi:10.1101/gad.14.3.366 · Cited by 152
Auto-Inhibition of Ets-1 Is Counteracted by DNA Binding Cooperativity with Core-Binding Factor α2
Goetz, T. L., Gu, T.-L., Speck, N. A., & Graves, B. J. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.1.81-90.2000 · Cited by 128
Structures of SAP-1 Bound to DNA Targets from the E74 and c-fos Promoters
Mo, Y., Vaessen, B., Johnston, K., & Marmorstein, R. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80130-6 · Cited by 103
“Site Selection Preferences by Ets Proteins conserved interactions with the GGA core sequence 23 22 21 1 2 3 4 5 6 (Kodandapani et al., 1996, 1998; Werner et al., 1997; SAP-1 A C C G G A At Ga Tc Batchelor et al., 1998), although the PU.1 protein (the Elk-1 A C C G G A A G T most divergent member of…”
BackgroundSzymczyna, B. R., & Arrowsmith, C. H. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004294200 · Cited by 99
The Structural and Dynamic Basis of Ets-1 DNA Binding Autoinhibition
Lee, G. M., Donaldson, L. W., Pufall, M. A., Kang, H.-S., Pot, I., Graves, B. J., & McIntosh, L. P. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m410722200 · Cited by 95
Fitzsimmons, D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.20.4154 · Cited by 39
Lionneton, F., Lelièvre, E., Baillat, D., Stehelin, D., & Soncin, F. (2003) · Oncogene · doi:10.1038/sj.onc.1207241 · Cited by 19
Metadata
- Authors
- Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J., & Gronenborn, A. M.
- Affiliations
- National Institutes of Health (US)
- Frederick National Laboratory for Cancer Research (US)
- National Institute of Diabetes and Digestive and Kidney Diseases (US)
- Venue
- Journal of Biomolecular NMR
- Published
- 1997-12
- Volume
- 10
- Issue
- 4
- Pages
- 317-328
- ISSN
- 0925-2738 (ISSN-L)
- 1573-5001
- OpenAlex
- W155985007
- Cited by
- 68
- References
- 46
- Citations by year
- 2023: 1 · 2022: 1 · 2021: 1 · 2020: 3 · 2018: 1 · 2017: 3 · 2016: 1 · 2015: 1 · 2014: 1 · 2013: 4 · 2012: 2
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Biomolecular NMR (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- ETS1, DNA-binding domain, protein-DNA complex, transcription factors, PU.1, intercalation, helix-turn-helix, major groove recognition, minor groove recognition, structure correction, NOE assignment, structure ensemble
- MeSH terms
- Amino Acid Sequence, Animals, DNA, DNA-Binding Proteins, Humans, Molecular Sequence Data, Magnetic Resonance Spectroscopy, Protein Binding, Proto-Oncogene Proteins, Transcription Factors, Crystallography, X-Ray, Proto-Oncogene Proteins c-ets, Proto-Oncogene Protein c-ets-1
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
