Primary Citation PubMed: 8413604
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MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.
(2005) Nucleic Acids Res 33
PubMed: 15991337 | PubMedCentral: PMC1160262 | DOI: null
Figure 2 Molecular graphics display of the four benchmark cases: ( a ) HIV-II protease complexed with its inhibitor L-735,524 (PDB ID: 1HSH); ( b ) FKBP-FK506, an immunophilin-immunosuppressant comple... (PDB ID: 1FKF); ( c ) Complex formed between phospholipase A2 and aspirin (PDB ID: 1OXR); and ( d ) TATA-box binding protein (YTBP) complexed with DNA containing a TATA-box (PDB ID: 1YTB).
( a ) HIV-II protease complexed with its inhibitor L-735,524 (PDB ID: 1HSH); ( b ) FKBP-FK506, an immunophilin-immunosuppressant complex (PDB ID: 1FKF); ( c ) complex formed between phospholipase A2 and aspirin (PDB ID: 1OXR); and ( d ) TATA-box binding protein (YTBP) complexed with DNA containing a TATA-box (PDB ID: 1YTB).
Publication Year: 2005
The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding.
(2007) Nucleic Acids Res 35
PubMed: 17426134 | PubMedCentral: PMC1885664 | DOI: 10.1093/nar/gkm144
The next highest similarity is found with the yeast TATA-box-binding protein (PDB code 1YTB, Z score = 5.7, r.m.s. deviation = 2.6 Å for 79 structurally... aligned residues, residues 4–12, 14–19, 21–27, 56–70, 124–132 and 134–166 of P. aeruginosa RdgC chain A and residues 69–96, 100–126 and 132–155 of TATA-box-binding protein, N-terminal half of chain A) ( 20 ).
Publication Year: 2007
Computer-based screening of functional conformers of proteins.
(2008) PLoS Comput Biol 4
PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009
TBP conformers with the highest and lowest values of both sensitivity and specificity in the four molecular dynamic simulations of TBP were used to show the relationship between the sensitivity value ... nd the RMSD of the conformer with respect to the 1YTB structure.
The complex of TBP bound to sequence 5′ GCGCGCGCGC 3′ (CG) was constructed introducing the necessary modifications to the 1YTB structure using the Biopolymer module of InsightII program.
The four simulations included: a) TBP+WtDNA, TBP in the presence of a high affinity substrate (the TATA sequence), using PDB file 1YTB  as the starting structure, b) TBP-WtDNA, TBP that was solved in the presence of the TATA sequence (that is 1YTB), but the DNA was not included in the simulation, c) TBP-GCDNA, TBP in the presence of a low affinity substrate (GC sequence) generated by in silico substitution of the TATA sequence present in 1YTB by the GCGCGCGCGC DNA duplex and d) TBP solved without substrate, using PDB file 1TBP  as a starting structure.
For TBP, the crystal structures used had the PDB codes: 1tbp for TBP without DNA, and 1ytb for the TBP complex with a TATA box (TATATAAA).
Publication Year: 2008
DNA conformations and their sequence preferences.
(2008) Nucleic Acids Res 36
PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260
The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
(2009) Nucleic Acids Res 37
PubMed: 19389725 | PubMedCentral: PMC2691843 | DOI: 10.1093/nar/gkp242
Such is the case for the TATA-binding protein (pdb: 1YTB ( 36 )), which binds to the minor groove of DNA and is known to achieve DNA sequence specificity through indirect readout.
Publication Year: 2009
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.
(2010) BMC Bioinformatics 11
PubMed: 20718956 | PubMedCentral: PMC2931518 | DOI: 10.1186/1471-2105-11-429
PDBcode Chain Length Rg S 1HCR A 52 6.92 0.504 1TGS I 56 6.25 0.137 1TGX A 60 6.84 0.158 1ISU A 62 6.02 0.203 1BF4 A 63 6.44 0.223 1PCF A 66 8.33 0.160 1B3A A 67 7.27 0.122 1ATZ A 75 7.24 0.214 1DP7 P... 76 7.35 0.237 3HTS B 82 7.02 0.286 3EIP A 84 7.35 0.233 2BOP A 85 7.90 0.122 1LMB 4 92 7.88 0.235 1FLT Y 94 7.55 0.132 1DIF A 99 7.82 0.260 1IIB A 103 7.38 0.228 1CMB A 104 8.35 0.116 256B A 106 8.37 0.245 1EVH A 111 7.78 0.180 1DPT A 117 8.56 0.194 1FLM B 122 8.26 0.118 2BBK L 124 8.05 0.317 1NWP A 128 7.88 0.179 1BBH A 131 9.18 0.161 1AQZ A 142 8.48 0.208 1A3A D 144 8.15 0.230 1M6P A 146 8.70 0.141 2TNF A 148 9.71 0.252 1ELK A 153 8.62 0.369 1NBC A 155 8.53 0.262 1DPS D 156 9.82 0.272 1PHN A 162 10.48 0.204 1C02 A 166 9.60 0.230 1YTB A 180 11.73 0.190 1BEH B 183 8.78 0.204 1ATL A 200 9.30 0.267 1BSM A 201 10.05 0.191 1YAC B 204 9.80 0.248 6GSV B 217 10.11 0.203 1AUO A 218 9.34 0.137 1QL0 A 241 9.59 0.165 1CYD A 242 10.13 0.287 1TPH 1 245 9.87 0.169 1A28 B 249 10.39 0.300 1C90 A 265 10.30 0.142 1AQU A 281 10.73 0.177 1BF6 B 291 10.21 0.294 1FTR A 296 12.14 0.295 4PGA A 330 11.67 0.217 1CZF A 335 11.43 0.241 S is the difference between the curves resulting from the two-body model and CRYSOL in units of "experimental" standard deviations.
Publication Year: 2010
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.
(2010) Nucleic Acids Res 38
PubMed: 20507912 | PubMedCentral: PMC2965220 | DOI: 10.1093/nar/gkq459
The DS C structure was constructed from the crystal structure of the TBP-bound TATA-box of sequence d(GTATATAAAACG) (PDB code 1YTB), extended by 6 bp at both extremities.
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
(2012) BMC Bioinformatics 13
PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165
Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH ... 000a0; Cro & repressor 1LMB Homeodomain 1FJL, 1HDD, 6PAX LacI repressor 1WET Endonuclease Fok1 1FOK Gamma Delta resolvase 1GDT Hin recombinase 1HCR RAP1 family 1IGN Prd paired domain 1PDN Tc3 transposase 1TC3 Trp repressor 1TRR Diptheria tox repressor 1DDN Transcription factor IIB 1D3U Interferon regulatory 2IRF Catabolite gene activator protein 1RUO Transcription factor 1CF7, 3HTS Ets domain 1BC8 Zinc Co-ordinating β-β-α zinc finger 1ZAA Harmone Nuclear Receptor 2NLL Loop sheet helix 1TSR GAL4 type 1ZME Zipper type Leucine Zipper 1YSA Helix loop helix 1AN2 Other-α Helix Pappilomavirus 1 E2 2BOP Histone 1AOI EBNA1 nuclear protein 1B3T Skn-1 transcription factor 1SKN Cre Recombinase 1CRX High Mobility Group 1QRV MADS box 1MNM β-Sheet TATA box binding 1YTB β-Hairpin/Ribbon MetJ repressor 1CMA Tus replication terminator 1ECR Integration host factor 1IHF Transcription Factor T-domain 1XBR Hyperthermophile DNA 1AZP Arc repressor 1PAR Other ReI homology 1SVC Stat protein 1BF5 Enzyme Methyltransferase 6MHT Endonuclease PvuII 3PVI Endonuclease ecorV 1RVA Endonuclease ecorI 1QPS Endonuclease BamHI 3BAM Enonuclease V 1VAS Dnase I 2DNJ DNA mismatch endonuclease 1CW0 DNA polymerase β 1BPY DNA Polymerase I 2BDP DNA Polymerase T7 1T7P,1CLQ HIV Reverse Transcriptase 2HMI Uracil DNA glycosylase 1SSP 3-Methyladenine DNA glycosylase 1BNK Homing endonuclease 1A73, 1BP7 TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).
Publication Year: 2012
Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.
(2014) PLoS One 9
PubMed: 24558431 | PubMedCentral: PMC3928310 | DOI: 10.1371/journal.pone.0088809
Taking this into account and in order to obtain a better convergence of the simulation, two kinked-DNA conformers were extracted from DNA-protein complexes available in the PDB (1A74, recognition DNA ... equence of I-PpoI  and 1YTB, yeast TATA-box) and were used as starting structures.
Publication Year: 2014
Making the bend: DNA tertiary structure and protein-DNA interactions.
(2014) Int J Mol Sci 15
PubMed: 25026169 | PubMedCentral: PMC4139847 | DOI: 10.3390/ijms150712335
The structure of the heptameric TATA box recognition sequence bound to TBP (PDB code 1YTB) shows that the protein only contacts the minor DNA groove and no base specific contacts occur.
Figure 11 DNA shape recognition of the TATA box by the TBP binding (PDB code 1YTB).
Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex.
(2014) Nat Struct Mol Biol 21
PubMed: 25132180 | PubMedCentral: PMC4219626 | DOI: 10.1038/nsmb.2873
The following structures were used to create the model: Pol I (Pdb, 4C2M) 15 , Rrn3 (Pdb, 3TJ1) 12 , A49-WH (Pdb, 3NFI) 19 , TBP (Pdb, 1YTB) 55 .
Accession Codes 4c2m, 3tj1, 3nfi, 4bbr, 2oit, 3hym, 1ytb References 1 Knutson BA Hahn S TFIIB-related factors in RNA polymerase I transcription.
PubMed ID is not available.
Published in 2015
For example, TBP protein binds to minor groove and partially unwinds and kinks DNA (PDB: 1YTB).
Publication Year: 2015
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
PubMed: 15673715 | PubMedCentral: PMC548349 | DOI: 10.1093/nar/gki204
Table 1 Data set of protein–DNA complexes Structural set (141 complexes) 1a02 1a0a 1a1g 1a1h 1a1k 1a3q 1akh 1am9 1an2 1an4 1apl 1au7 1b01 1b3t 1b72 1b8i 1bc8 1bdt 1bf5 1bl0 1by4 1c0w 1c9b 1cdw... 1cez 1cf7 1cgp 1cit 1d3u 1d5y 1ddn 1dh3 1du0 1dux 1e3o 1ea4 1efa 1egw 1f2i 1f5t 1fjl 1fos 1fzp 1g2f 1gd2 1gji 1gt0 1gu4 1gu5 1gxp 1h6f 1h8a 1h9d 1h9t 1hbx 1hcq 1hlo 1hlz 1hw2 1hwt 1ic8 1if1 1ig7 1ign 1imh 1io4 1j59 1je8 1jfi 1jgg 1jj4 1jk1 1jk2 1jnm 1jt0 1k6o 1k78 1k79 1k7a 1kb2 1kb4 1kb6 1ku7 1l3l 1lat 1lb2 1le5 1le9 1llm 1lmb 1lq1 1mdy 1mhd 1mjm 1mjo 1mm8 1mnm 1mnn 1mur 1n6j 1ngm 1nkp 1nvp 1nwq 1oct 1odh 1owf 1p47 1p7h 1pdn 1per 1pp7 1pp8 1pue 1puf 1pyi 1pzu 1r0o 1r4o 1r4r 1ram 1rio 1rpe 1run 1skn 1tf6 1tgh 1tsr 1ubd 1yrn 1ysa 1ytb 1ytf 2cgp 2drp 2gli 2hap 2hdd 2or1 6cro 6pax Table 2 Recognition accuracy for specific interactions between TFs and native bound DNA sequences Accuracy Top 1(%) Top 10(%) Top 20(%) Top 1(%) Top 5(%) Whole structural set 39.7 70.2 77.3 79.4 90.1 α-Helix a 26.3 54.4 63.2 66.7 82.5 α-Helix + β-strand a 49.4 79.2 85.7 87.0 94.8 a α-helix and β-strand refer to the secondary structures of DNA-binding sites.
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