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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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PDB ID Mentions in PubMed Central

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.

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Evolutionary conservation of DNA-contact residues in DNA-binding domains.

(2008) BMC Bioinformatics 9 Suppl 6

PubMed: 18541056 | PubMedCentral: PMC2423444 | DOI: 10.1186/1471-2105-9-S6-S3

According to z-scores, these 13 domains can be roughly divided into two groups, including the Ubx-like homeodomain colored in blue (e.g. PDB entry 9ANT-A (12.77), 1AHD-P (12.19), and 1SAN (11.96)) and... the Oct-1 POU homeodomain colored in red (e.g. PDB entry 1E3O-C1 (6.40), 1GT0-C1 (6.38), and 1O4X-A1 (4.40)).

Publication Year: 2008


Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.

(2009) Nucleic Acids Res 37

PubMed: 19304746 | PubMedCentral: PMC2691818 | DOI: 10.1093/nar/gkp157

( A ) Structural superposition of box B of h-mtTFA (3fgh; red) overlaid with HMGD (1qrv; yellow), UBF box 5 (2hdz; green), LEF1 (2lef; purple), HMGB1 box A (1ckt; cyan) and Sox2 (1gt0; black).

Overall RMSD values were calculated between each amino acid of the structures of HMGD [PDB ID 1qrv ( 36 )], SOX2 HMG box A (PDB ID 1gt0, Remenyi, A., Scholer, H.R., Wilmanns, M. unpublished), HMGB1 box A [PDB ID 1ckt ( 37 )], LEF1 [PDB ID 2lef ( 38 )] and UBF5 [PDB ID 2hdz; Rong, H., Teng, M.K., and Niu, L., unpublished data)] and the X-ray crystal structure of h-mtTFA box B using the program COOT ( 33 ).

Publication Year: 2009


The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.

(2011) Nat Struct Mol Biol 18

PubMed: 22037171 | PubMedCentral: PMC3210390 | DOI: 10.1038/nsmb.2159

Structures correspond to the following accession numbers, and RMSD values, relative to HMG-box A of Tfam, are provided in parentheses: HMG-box B of Tfam without DNA, 3fgh 19 (0.974); Hmgb1 box A, 1ckt... 27 (1.101); Lef1, 2lef 28 (1.162); Sox2, 1gt0 29 (1.152); Hmgd, 1qrv 30 (1.127).

Publication Year: 2011


Deciphering the Sox-Oct partner code by quantitative cooperativity measurements.

(2012) Nucleic Acids Res 40

PubMed: 22344693 | PubMedCentral: PMC3367189 | DOI: 10.1093/nar/gks153

Structural modeling and analysis Homology models for Sox HMG or the Oct4 POU domain proteins were generated using I-TASSER with the Sox17 HMG (pdb-id 3F27) and the Oct1 POU (pdb-id 1GT0) as templates ... http://zhanglab.ccmb.med.umich.edu/I-TASSER/ ) ( 28 ).

Publication Year: 2012


A disorder-to-order structural transition in the COOH-tail of Fz4 determines misfolding of the L501fsX533-Fz4 mutant.

(2013) Sci Rep 3

PubMed: 24036468 | PubMedCentral: PMC3773625 | DOI: 10.1038/srep02659

The loop is predicted for the structural similarity with helix-loop-helix containing proteins like transcription factors and calcium binding proteins [PDB: 1R9D 23 , 3FGH 24 , 1GT0 25 ].

Publication Year: 2013


Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis.

(2013) Comput Math Methods Med 2013

PubMed: 24324527 | PubMedCentral: PMC3845252 | DOI: 10.1155/2013/854710

Figure 1(a) displays the 3D structure of complex 1GT0 and the diagram is produced using UCSF Chimera [ 19 ].

Experimental Data Two POU/HMG/DNA ternary complexes, 1GT0 and 1O4X, are downloaded from the Protein Data Bank (PDB) [ 18 ] for analysis.

Publication Year: 2013


Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24914984 | PubMedCentral: PMC4051508 | DOI: 10.1107/S1399004714007603

  TFZ CC (%) MPE (°) Full models with DNA and protein with side chains  1akh 9.83 10.11 89.50  1au7 9.65 9.53 89.20  1b8i 9.03 9.49 89.40  1du0 9.67 10.... 2 89.20  1fjl 9.18 9.47 89.50  1gt0 9.17 8.83 89.20  1yrn 9.93 9.74 89.10  2d5v 8.88 9.16 89.30  2h1k 9.28 9.12 89.40  2hdd 9.18 8.78 89.40  2r5z 9.53 9.23 89.30  9ant 8.76 9.69 89.50 Full models with DNA and protein without side chains  1akh 10.12 8.90 89.30  1au7 9.68 9.43 89.30  1b8i 10.25 8.54 89.30  1du0 8.74 8.90 89.50  1fjl 9.61 9.12 89.10  1gt0 9.84 8.58 90.00  1yrn 10.28 8.39 89.10  2d5v 9.88 8.57 89.80  2h1k 9.06 9.05 89.30  2hdd 7.90 10.27 89.50  2r5z 9.54 8.89 89.40  9ant 8.56 9.31 89.50 Models without DNA, protein with side chains  1fjl 8.92      1yrn 8.23      2d5v 8.24      2h1k 10.39      2hdd 8.13      2r5z 9.82      9ant 8.62     Models without DNA, protein without side chains  2h1k 11.04     Models with DNA, only one helix of the protein with side chains  1akh 11.20 8.61 89.30  1au7 9.73 8.95 89.30  1b8i 9.68 9.61 89.40  1du0 9.26 8.93 89.30  1fjl 10.24 9.56 89.50  1gt0 10.17 9.51 89.20  1yrn 10.86 9.10 89.40  2d5v 10.20 9.19 89.50  2h1k 10.58 8.97 89.50  2hdd 9.57 8.96 89.20  2r5z 10.46 9.70 88.80  9ant 10.68 10.10 89.40 Models with DNA, only one helix of the protein without side chains  1akh 10.62 9.70 89.30  1au7 10.38 9.49 88.80  1b8i 10.35 9.56 89.50  1du0 10.20 9.56 89.50  1fjl 9.80 9.49 89.70  1gt0 11.50 8.79 89.40  1yrn 10.97 8.54 89.60  2d5v 11.25 9.26 89.40  2h1k 11.07 9.76 89.40  2hdd 8.93 9.32 89.20  2r5z 10.44 8.83 89.60  9ant 10.70 8.87 89.40 Ideal helix (after location of one fragment)   11.36     Perfect fragment (DNA + HTH motif)     27.90 41.5

( e ) The same HTH fragments as in ( d ) but with polyalanines; one two-helix bundle HTH fragment with polyalanine side chains only solves in the case of 1gt0 .

( b ) HTH fragments without truncation (31–33 amino acids, 7–8 bp); all but one ( 1gt0 ) solve the target structure 3RKQ .

  TFZ CC (%) MPE (°) Full models with DNA and protein with side chains (31–33 amino acids and 7–8 bp)  1akh 6.35 31.49 33.50  1au7 6.78 30.37 33.60  1b8i 10.57 30.55 33.50  1du0 18.08 30.94 33.80  1fjl 15.27 30.49 33.40  1gt0 7.01 8.83 90.20  1yrn 14.88 30.66 33.70  2d5v 11.84 31.01 33.90  2h1k 18.07 31.93 33.50  2hdd 15.20 30.45 33.60  2r5z 12.46 30.19 34.00  9ant 19.66 30.57 33.70 Full models with DNA and protein without side chains (31–33 amino acids and 7–8 bp)  1akh 6.59 9.51 89.40  1au7 7.46 30.53 33.80  1b8i 8.49 31.08 33.30  1du0 16.38 30.46 33.30  1fjl 11.83 30.97 33.50  1gt0 7.32 9.96 89.00  1yrn 10.69 31.05 33.70  2d5v 12.13 31.48 33.40  2h1k 14.63 30.23 33.40  2hdd 10.87 31.01 33.40  2r5z 11.46 30.86 34.00  9ant 19.58 30.33 33.90 Models without DNA, protein with side chains (31–33 amino acids)  1akh 10.58 30.00 34.20  1au7 6.33 10.74 88.90  1b8i 13.22 30.95 33.70  1du0 6.51 11.27 73.60  1fjl 6.62 9.94 89.50  1gt0 7.83 31.06 33.40  1yrn 10.98 31.22 33.60  2d5v 6.54 30.29 33.50  2h1k 10.37 31.04 33.90  2hdd 6.64 11.37 88.50  2r5z 6.75 29.71 33.80  9ant 11.51 30.64 34.10 Models without DNA, protein without side chains (31–33 amino acids)  1akh 6.86 10.49 89.50  1au7 7.00 11.13 89.40  1b8i 6.62 10.27 89.40  1du0 6.11 10.25 89.20  1fjl 6.68 10.91 89.50  1gt0 8.79 31.34 33.30  1yrn 7.07 10.71 89.70  2d5v 6.84 11.06 89.30  2h1k 6.35 10.44 89.10  2hdd 6.49 11.07 89.50  2r5z 7.74 10.24 89.10  9ant 7.67 10.86 89.30 Models with DNA, only one helix of the protein with side chains (15–17 amino acids and 7–8 bp)  1akh 7.29 31.33 33.30  1au7 8.05 30.96 33.60  1b8i 8.85 30.45 33.90  1du0 16.02 30.46 33.40  1fjl 8.10 30.27 33.30  1gt0 7.64 31.16 33.60  1yrn 10.72 30.90 33.60  2d5v 11.25 30.38 33.90  2h1k 15.96 31.12 33.40  2hdd 13.06 30.53 33.60  2r5z 10.29 30.71 33.50  9ant 15.90 30.57 33.60 Models with DNA, only one helix of the protein without side chains (15–17 amino acids and 7–8 bp)  1akh 6.75 9.78 89.30  1au7 10.01 30.44 33.30  1b8i 7.07 11.14 89.10  1du0 14.17 31.28 33.80  1fjl 7.64 11.29 89.20  1gt0 7.18 9.77 89.60  1yrn 6.98 9.82 89.40  2d5v 11.20 30.96 33.70  2h1k 11.45 30.92 33.50  2hdd 10.02 29.89 34.10  2r5z 7.91 30.73 33.50  9ant 14.09 31.54 33.10 Ideal helix (14 amino acids; after location of two fragments)   8.69 31.43 33.20 Table 3 ARCIMBOLDO results for HTH proteins for several approaches to solving the target structure 3PVV with the fragment models The TFZ, CC and MPE values for solutions are given in bold; results are shown after location of two fragments with Phaser .

( c ) HTH fragments with same number of residues as in ( a ) but with all side chains set to polyalanine; all models except 1akh and 1gt0 solve the target structure.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4330359

Homology modeling of Sox2–Pax6 The models of the Sox2–Pax6–DNA ternary complexes were build by superimposing B-DNA fragments corresponding to the DC5, N3 and DC5con sequences o... the N-terminus and C-terminus of the structures of the Sox2/DNA and Pax6/DNA complexes, 1GT0 ( 13 ) and 6PAX ( 30 ), respectively.

Accession Numbers 6PAX and 1GT0.

The Sox2-HMG derived from PDB-ID 1GT0( 13 )is shown in blue and the Pax6-PRD (PDB-ID 6PAX ( 30 )) in orange.

( E ) CSP of Sox2 in binary (orange) and ternary (green) complexes relative to free Sox2 versus the Sox2 amino acid sequence (numbered according to Sox2: PDB 1GT0 ( 13 )).

Publication Year: 2015


Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

(2005) Nucleic Acids Res 33

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.

Publication Year: 2005