Primary Citation PubMed: 12079378
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.
(2006) Nucleic Acids Res 34
PubMed: 16641317 | PubMedCentral: PMC1449907 | DOI: 10.1093/nar/gkl182
MATERIALS AND METHODS The Oxytricha nova d(G 4 T 4 G 4 ) 2 crystal structure ( 9 ) was used as a template for diagonal loop quadruplexes (PDB code 1JPQ).
Publication Year: 2006
Quadruplex DNA: sequence, topology and structure.
PubMed: 17012276 | PubMedCentral: PMC1636468 | DOI: 10.1093/nar/gkl655
Figure 3 The crystal structure ( 28 ) of the bimolecular quadruplex formed by the O.nova telomeric sequence d(G 4 T 4 G 4 ) (PDB entry 1JPQ).
Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.
(2007) Nucleic Acids Res 35
PubMed: 17720713 | PubMedCentral: PMC2034477 | DOI: 10.1093/nar/gkm609
The G17–G18 stacking in the loop is similar to that found in the T4-T5 stacking adopted in the loop region of the crystal structure of the Oxytricha telomeric sequence G 4 T 4 G 4 (40: PDB id ... JPQ).
Publication Year: 2007
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 ).
The central step of the quadruplex (Residues 2 and 3) in complexes with the telomere-end binding protein [structures 1JB7 ( 74 ), 1PH4, 1PH6 and 1PH8 ( 56 )] as well as in the non-complexed quadruplex [1JPQ ( 75 )] adopts the conformation of Cluster 122 ( Supplementary Table T2 ), a B-like cluster with the canonical α + 1 and γ + 1 values flipped (‘α + 1/γ + 1 crank’) and with the syn orientation (χ ∼ 70°) of the second guanine base enabling non-W–Ck purine–purine base pair.
Publication Year: 2008
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
(2011) Nucleic Acids Res 39
PubMed: 21296760 | PubMedCentral: PMC3105399 | DOI: 10.1093/nar/gkr031
The coordinates of the first and the second quartets with sandwiched K + ions were obtained from the crystal structure of the diagonal anti-parallel G-quadruplex [d(G 4 T 4 G 4 )] 2 [( 33 ); PDB: 1JPQ... and were used as the initial structure for the SA-aabb model.
Publication Year: 2011
Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.
(2011) J Am Chem Soc 133
PubMed: 21761922 | PubMedCentral: PMC3168932 | DOI: 10.1021/ja107805r
( 56 ) Methods Starting Structures All of the L n , L w , D , and P 3 a models were built from the NMR structure 2GKU ;( 56 ) the P 2 a models were built from the 1L34 structure;( 57 ) the P 4 a stems... were built from the crystal structure 1JPQ with two loop K + ions removed from the initial structure;( 58 ) and the stem structures of the P 3 p / P 4 p models were obtained from the first three/four G-quartets of the 139D structure, respectively.
The T 4 - models were all built from the loop present in the 1JPQ structure.
Thrombin-aptamer recognition: a revealed ambiguity.
PubMed: 21715374 | PubMedCentral: PMC3177225 | DOI: 10.1093/nar/gkr522
A brief analysis of other quadruplex structures (PDB codes: 2AVH, 1JPQ, 1I34) shows that this type of interaction is not unusual in antiparallel quadruplex, where guanine residues with syn and anti co... formations alternate along the strand.
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.
(2013) Nucleic Acids Res 41
PubMed: 23700306 | PubMedCentral: PMC3737530 | DOI: 10.1093/nar/gkt412
Six of them were taken from the Protein Data Bank (PDB): (i) the nuclear magnetic resonance (NMR) solution structure of d[T 2 (G 3 T 2 A) 3 G 3 A] (2GKU, first frame) ( 12 ), a 3+1 (hybrid) monomolecu... ar quadruplex with three tetrads; (ii) the X-ray structure of d[A(G 3 T 2 A) 3 G 3 ] (1KF1) ( 45 ) folded in a monomolecular parallel quadruplex with three tetrads; (iii) the X-ray structure of [d(G 4 T 4 G 4 )] 2 (1JPQ) ( 46 ) Oxytricha nova telomeric dimeric antiparallel quadruplex with four tetrads; (iv) the X-ray structure of [d(TG 4 T)] 4 (352D) ( 47 ), forming four consecutive parallel stranded guanine tetrads with thymidines unstructured and bulged into space (one disordered thymidine residue was modeled); (v) the structure of RNA parallel quadruplex [r(UG 4 U)] 4 (1J8G) ( 48 ), forming four G-tetrads complemented by uridines that are bulged out; and (vi) the X-ray structure of [d(G 4 )] 4 (3TVB) ( 49 ), forming a parallel stranded stem with the first tetrad all- syn .
Publication Year: 2013
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.