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PDB ID Mentions in PubMed Central Article count: 29

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PDB ID Mentions in PubMed Central

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Protein-DNA binding specificity predictions with structural models.

(2005) Nucleic Acids Res 33

PubMed: 16246914 | PubMedCentral: PMC1270944 | DOI: 10.1093/nar/gki875

Table 4 Summary of binding site energy predictions PDB Z PDB 〈 Z site 〉 Rank L 1mnn −3.69 −2.54 14 12 1ysa −3.38 −2.53 1 7 1yrn −4.30 −3... 34 – 19 1aay −3.70 −3.60 13 10 1b8i −3.22 −2.74 8 10 1r0o −3.80 −2.88 – 15 2drp −3.77 −2.76 6 11 1yui −2.38 −2.48 91 7 1fjl −3.22 −2.93 4507 13 1gxp −4.17 −3.06 – 20 1ihf −3.41 −1.12 – 34 1j1v −4.20 −3.36 13 13 1mj2 −3.09 −2.13 – 16 1run −3.50 −2.32 – 22 1tro −3.73 −2.57 – 18 2puc −3.88 −3.68 – 16 Z PDB is the Z -score ( Equation 16 ) for the protein–DNA binding energy with the binding site found in the protein–DNA structure; 〈 Z site 〉 is the average Z -score for protein–DNA binding energies with binding sites listed in Table 2 ; Rank is the rank of the binding energy for the structural site in the ensemble of 4 L sequences ( L is the binding site length).

Table 1 Experimental binding affinity dataset Name PDB code Method (Res., Å) ΔΔ G data points Organism Reference Zif268 1aay X-ray (1.6) 15 (8) Mus musculus ( 42 ) Zif268 1aay X-ray (1.6) 6 (6) M.musculus ( 67 ) Zif268 D20A 1jk1 X-ray (1.9) 6 (6) M.musculus ( 67 ) Tus 1ecr X-ray (2.7) 20 (20) Escherichia coli ( 68 ) LacR 1efa X-ray (2.6) 5 (5) E.coli ( 69 ) λR 1lmb X-ray (1.8) 51 (51) λ-Phage ( 51 ) TrpR 1tro X-ray (1.9) 9 (9) E.coli ( 70 ) ER 1hcq X-ray (2.4) 7 (7) Homo sapiens ( 71 ) CroR 6cro X-ray (3.0) 56 (56) λ-Phage ( 52 ) EcoRI 1ckq X-ray (1.85) 13 (13) E.coli ( 41 ) Crp 1run X-ray (2.7) 15 (15) E.coli ( 72 ) BamHI 1bhm X-ray (2.2) 23 (0) Bacillus amyloliquefaciens ( 49 ) PU.1 ETS 1pue X-ray (2.1) 25 (0) M.musculus ( 50 ) Ndt80 1mnn X-ray (1.4) 26 (0) Saccharomyces cerevisiae ( 34 ) MAT a 1/α2 1yrn X-ray (2.5) 54 (0) S.cerevisiae ( 30 ) c-Myb 1mse NMR (NA) 27 (0) M.musculus ( 47 ) AtERF1 1gcc NMR (NA) 21 (0) Arabidopsis thaliana ( 45 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

Table 2 Experimental binding site and weight matrix dataset Name PDB code Method (Res., Å) N seq Organism Reference λR 1lmb X-ray (1.8) – a λ-Phage ( 51 ) CroR 6cro X-ray (3.0) – a λ-Phage ( 52 ) AtERF1 1gcc NMR (NA) – a A.thaliana ( 45 ) c-Myb 1mse NMR (NA) – a M.musculus ( 47 ) Zif268 1aay X-ray (1.6) 6 b M.musculus ( 31 ) Ndt80 1mnn X-ray (1.4) 8 b S.cerevisiae ( 34 ) Gcn4p 1ysa X-ray (2.9) 9 c S.cerevisiae ( 35 , 36 ) MAT a 1/α2 1yrn X-ray (2.5) 19 c S.cerevisiae ( 30 ) EcR/Usp 1r0o X-ray (2.24) 33 c Drosophila melanogaster ( 57 ) Ttk 2drp X-ray (2.8) 16 c D.melanogaster – Prd(homeo) 1fjl X-ray (2.0) 15 c D.melanogaster ( 37 ) Ubx/Exd 1b8i X-ray (2.4) 4 b D.melanogaster – Trl 1yui NMR (NA) 5 c D.melanogaster – MetJ 1mj2 X-ray (2.4) 16 c E.coli ( 32 ) TrpR 1tro X-ray (1.9) 15 c E.coli ( 32 , 33 ) PhoB 1gxp X-ray (2.5) 16 c E.coli ( 32 ) Ihf 1ihf X-ray (2.5) 27 c E.coli ( 32 ) DnaA 1j1v X-ray (2.1) 9 c E.coli ( 32 ) PurR 2puc X-ray (2.7) 23 c E.coli ( 32 ) Crp 1run X-ray (2.7) 50 c E.coli ( 32 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

Publication Year: 2005

An overview of the structures of protein-DNA complexes.

(2000) Genome Biol 1

PubMed: 11104519 | PubMedCentral: PMC138832 | DOI: 10.1186/gb-2000-1-1-reviews001

In this review, structures are identified by the standard four-digit PDB code (for example, 1aay).

Publication Year: 2000

Energetics of protein-DNA interactions.

(2007) Nucleic Acids Res 35

PubMed: 17259221 | PubMedCentral: PMC1851630 | DOI: 10.1093/nar/gkl1103

The full set includes 189 mutants from ten structures: 1aay, 1ckq, 1ecr, 1efa, 1hcq, 1jk1, 1lmb, 1run, 1tro and 6cro.

The set then contains the following 30 structures: 1aay, 1apl, 1az0, 1azp, 1bc7, 1bhm, 1bp7, 1ca5, 1cdw, 1cma, 1cw0, 1ecr, 1efa, 1glu, 1hcq, 1hcr, 1ihf, 1ipp, 1lmb, 1mdy, 1nfk, 1oct, 1par, 1pue, 1qrv, 1run, 1tro, 1tsr, 1ysa and 1ytf.

Publication Year: 2007

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

(2007) Nucleic Acids Res 35

PubMed: 17264128 | PubMedCentral: PMC1851644 | DOI: 10.1093/nar/gkl1155

C 2 H 2 ZF-DNA PDB files PDB code Chains Description Res (Å) Topology a 1llm C,D Zif268-GCN4 (dimer) 1.5 2_3:3_2 1aay A Zif268 1.6 3_2_1 1a1f, 1a1g, 1a1h, 1a1i, 1a1j, 1a1k, 1a1l A Zif268 (Fn1 ... utants) 1.6 3_2_1 1jk1, 1jk2 A Zif268 (Fn1 D20A) 1.9 3_2_1 1zaa C Zif268 2.1 3_2_1 1mey C,F Designed 2.2 3_2_1 1g2d, 1g2f C,F Designed 2.2 3_2_1 1p47 A,B Zif268 tandem 2.2 3_2_1 3_2_1 1f2i G,H,I,J,K,L Zif268-extension (dimer) 2.4 2_1:1_2 1ubd C YY1 (Yin Yang 1) 2.5 4_3_2_1 2gli A GLI (glioblastoma) 2.6 5_4_3_2_1 2drp A,D Tramtrack 2.8 2_1 1tf6 A,D TFIIIA n/a (NMR) 6_5_4_3_2_1 a Topology description for the individual ZF domains; 3_2_1 indicates a polydactyl ZF protein with three ZF domains, 1 refers to the N-terminal ZF domain.

Worm representation of ZF helix residues (canonical numbering 1–11) are shown for four ZF2 domains: two wild-type Zif268 proteins, 1aay/hrZif268 (gray) and 1zaa (red); and two modified Zif268 proteins, 1llm chain C (yellow) and 1f2i chain K (blue).

Side-chain conformations for the His residue at canonical ZF position 3 are shown from hrZif268 ZF2 (1aay His149; white), and from the complexes modeled with the TGG sequence (red) and TTG sequence (brown) using hrZif268 ZF2 as a template.

In the case of the Zif268 ZF2 domain discussed here, we found that not including the hydrogen bonding term did not greatly affect predictions when the 1.6 Å Zif268 structure (1aay) was used as a template.

For example, when the modeled bases were assumed to be co-planar with those in the 1.6 Å Zif268 template structure (1aay), the AGG sequence (see Table 3 ) was no longer ranked in the top eight.

Base identities appear as in the PDB file 1aay.

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 ).

Publication Year: 2008

Insights into protein-DNA interactions through structure network analysis.

(2008) PLoS Comput Biol 4

PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170

Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).

Publication Year: 2008

Prediction of TF target sites based on atomistic models of protein-DNA complexes.

(2008) BMC Bioinformatics 9

PubMed: 18922190 | PubMedCentral: PMC2585596 | DOI: 10.1186/1471-2105-9-436

Table 3 Comparison of cumulative contact and readout position weight matrices for 4 prokaryotic (top) and 4 eukaryotic (bottom) transcription factors SCOP v1.73 superfamily TF [PDB id ] Resolution (&#... 000c5;) R obs E -value contacts E -value readout Winged helix CRP [1cgp] 3 0.24 7.93E-03 3.76E-05 C-terminal domain of the bipartite response regulators NarL [1je8] 2.12 0.23 3.58E-05 7.01E-07 lambda repressor-like DNA-binding domains PurR [2pua] 2.9 0.16 4.33E-15 5.51E-01 (7.58E-04) ribbon-helix-helix MetJ [1cma] 2.8 0.22 1.22E-01 3.30E-01 Zn2/Cys6 DNA-binding domain LEU3 [2er8] 2.85 0.23 4.97E-06 5.52E-05 HLH, helix-loop-helix DNA-binding domain PHO4 [1a0a] 2.8 0.23 3.57E-07 3.97E-07 Homeodomain-like RAP1 [1ign] 2.25 0.21 5.52E-03 1.89E-02 (6.40E-04) C2H2 and C2HC zinc fingers ZIF268 [1aay] 1.6 0.19 7.93E-14 1.99E-14 In the first column we include the name of the structural superfamily of each TF according to SCOP [ 37 ].

Publication Year: 2008

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

Optimization of specificity and affinity in the C2H2 zinc finger family C2H2 zinc finger family (pdb codes: 1zaa, 1aay, 1mey, 1ubd, 1g2f, 1a1f, 1a1h, 1a1j) Position Counts 〈 opt.

Publication Year: 2009

Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.

(2009) Nucleic Acids Res 37

PubMed: 19429892 | PubMedCentral: PMC2709573 | DOI: 10.1093/nar/gkp289

−1 (PDB code: 1AAY) ( 38 ); (ii) Q mode from QGSR/GCA mutant (PDB code: 1A1H) shows that Q −1 can reach closer to the DNA forming a bond with A +1 if there is also a single matching bo... d at Pos.

DNA triplets are taken from crystals, i.e. PDB codes 1AAY ( 38 ), 1A1F ( 37 ), 1A1H ( 37 ), 1MEY ( 42 ), 1MDM ( 43 ), 1A1L/1A1J ( 37 ), 1MDY ( 44 ) and 2I13 ( 45 ), and to assure the continuity of the DNA chain the triplets are simply superimposed to the backbone of the appropriate binding mode.

Publication Year: 2009

Cavities in protein-DNA and protein-RNA interfaces.

(2009) Nucleic Acids Res 37

PubMed: 19494181 | PubMedCentral: PMC2724294 | DOI: 10.1093/nar/gkp488

Three interface cavities in the structure of a zinc finger protein (PDB file, 1aay), with three domains, assigned using SCOP ( 43 ), shown in distinct colors.

Publication Year: 2009

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.

(2010) Nucleic Acids Res 38

PubMed: 20047959 | PubMedCentral: PMC2853105 | DOI: 10.1093/nar/gkp1132

( A ) Cartoon of EGR bound to DNA [PDB code: 1AAY ( 39 )].

Mouse early growth response (EGR) factor EGR factor ( 39 ) (Protein Data Bank (PDB) code 1AAY) protein has three ZFs ( Figure 1 A).

Publication Year: 2010

Integration of open access literature into the RCSB Protein Data Bank using BioLit.

(2010) BMC Bioinformatics 11

PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220

of Articles 1JJ2 Large Ribosomal Subunit 27 1J5E 30S Ribosomal Subunit 19 1FFK Large Ribosomal Subunit 19 1LMB Lambda Repressor 19 1AAY Zinc Finger 17 1TSR P53 16 1F88 Rhodopsin 15 1BRS Barnase/Barsta... complex 14 The open access literature for RCSB PDB entries is available from the Literature tab for each structure entry at .

Publication Year: 2010

THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.

(2010) Nat Struct Mol Biol 17

PubMed: 20010837 | PubMedCentral: PMC2933787 | DOI: 10.1038/nsmb.1742

Cartoon representation of a) DmTHAP and b) Zif268 (PDB ID: 1AAY 32 ) in association with double-stranded DNA.

Publication Year: 2010

Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example.

(2010) Nucleic Acids Res 38

PubMed: 20685816 | PubMedCentral: PMC2995082 | DOI: 10.1093/nar/gkq683

The cases where FoldX performs better than the dynamic model are shown in green, otherwise in red 1AAY and 1JK1 are considered together in Morozov et al. ( 24 ).

Publication Year: 2010

Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.

(2010) BMC Struct Biol 10

PubMed: 21106075 | PubMedCentral: PMC3002361 | DOI: 10.1186/1472-6807-10-42

PDB Code Aminoacid sequence at positions -1, 2, 3, 6 Nucleotidic sequence at positions 8-11 Dissociation Constant (Kd, nM) 1A1F DSNR GACC 0.019 1A1G DSNR GCGT (wild type) 1.8 1A1I RADR GCAC 0.068 1A1J... RADR GCGT (wild type) 0.035 1A1K RADR GACC 9.3 1A1L RDER (wild type) GCAC 5.6 1AAY RDER (wild type) GCGT (wild type) 2.7 This table reports on the names of the complexes, the specific sequences on Helix 1 that recognize DNA, DNA sequences, and the respective dissociation constants.

PDB Code Aminoacid sequence at positions -1, 2, 3, 6 Kd (nM) Total Protein Flexibility (RMSF sum (nm)) Total Complex Flexibility (RMSF sum (nm)) 1A1F DSNR 0.019 7.18 9.49 1A1G DSNR 1.8 6.05 8.70 1A1I RADR 0.068 7.72 9.03 1A1J RADR 0.035 7.6 10.1 1A1K RADR 9.3 5.87 8.38 1A1L RDER (wild type) 5.6 6.10 7.97 1AAY RDER (wild type) 2.7 6.47 8.68 Correlation Log(Kd)/RMSF -0.92 -0.88 The complexes simulated, the dissociation constants, the total flexibility of each system evaluated as a sum of the Root Mean Square Fluctuations (RMSFs) of the proteins and of the complexes are indicated.

PDB Code Protein-Protein Protein-DNA DNA-DNA Total Stabilization Energy Intra-protein 1A1F -58,47 -414,60 -734,92 -1207,99 -513,38 1A1G -64,77 -432,7 -722,54 -1220,01 -390,68 1A1I -65,75 -433,5 -714,52 -1213,77 -367,53 1A1J -66,12 -438,35 -726,55 -1231,02 -440,24 1A1K -61,61 -423,81 -728,83 -1214,25 -137,19 1A1L -89,11 -501,37 -705,23 -1295,71 -210,41 1AAY -64,44 -432,67 -726,34 -1223,45 -342,07 Energetic contributions calculated according to the Energy Decomposition Method due to intraprotein, protein-DNA and intra-DNA contributions are indicated.

Publication Year: 2010

Towards computational specificity screening of DNA-binding proteins.

(2011) Nucleic Acids Res 39

PubMed: 21737424 | PubMedCentral: PMC3201868 | DOI: 10.1093/nar/gkr531

Simulations were started from the X-ray structure of Zif268 bound to DNA [PDB entry 1AAY ( 44 )].

Publication Year: 2011

Zinc-finger recombinase activities in vitro.

(2011) Nucleic Acids Res 39

PubMed: 21849325 | PubMedCentral: PMC3241657 | DOI: 10.1093/nar/gkr652

The model is built from the resolvase–DNA structure 1GDT and two copies of the Zif268 domain–DNA structure 1AAY.

The right panel shows a ZFR synaptic tetramer, built from four copies of 1AAY and the resolvase synaptic complex structure 1ZR4.

Note that E2, the first residue of the Zif268 domain in the ZFRs ( Figure 2 B), could not be used for the measurements as it was not resolved in the 1AAY crystal structure.

Molecular modelling Models of ZFRs bound to Z-sites with different core sequence lengths were built in PyMol ( 23 ) using crystal structures of a γδ resolvase dimer–DNA complex [1GDT; ( 24 )], a synaptic γδ resolvase–DNA intermediate [1ZR4; ( 25 )] and a Zif268 zinc-finger domain–DNA complex [1AAY; ( 26 )].

Publication Year: 2011

Benchmarks for flexible and rigid transcription factor-DNA docking.

(2011) BMC Struct Biol 11

PubMed: 22044637 | PubMedCentral: PMC3262759 | DOI: 10.1186/1472-6807-11-45

(Å) SCOP Protein Oligo_state DNA NRBC b BSA(Å 2 ) c ZIF268 1aay 1.60 g.37.1.1 A Monomer B, C 13 960.81 Max 1an2 2.90 a.38.1.1 A, C Homodimer B, D 10 933.75 Papillomavirus E2 1jj4 2.40 ... .58.8.1 A, B Heterodimer C, D 10 839.96 QacR 1jt0 a 2.90 a.4.1.9 B, D Homodimer E, F 12 1085.51 Lambda repressor 1lmb 1.80 a.35.1.2 3, 4 Homodimer 1, 2 10 1105.4 TATA-binding 1qn4 1.86 d.129.1.1 B Monomer E, F 15 1107.51 Tet repressor 1qpi 2.50 a.4.1.9 A, C Homodimer B, M 14 973.49 MecI 1sax 2.80 a.4.5.39 A, B Homodimer C, D 12 1130.16 Trep repressor 1tro a 1.90 a.4.12.1 A, C Homodimer I, J 12 1243.06 OhrR 1z9c 2.64 a.4.5.28 C, D Homodimer I, J 12 1669.81 Easy Phi lambda phage cII 1zs4 1.70 a.39.1.9 A, B, C, D HT d U, T 14 1043.06 p53 2ac0 1.80 b.2.5.2 A, B, C, D HT d E, F, G, H 21 1921.76 CAP 2cgp 2.20 a.4.5.4 A, F Homodimer B, C, D, E 10 944.43 LRP/ASNC family protein 2e1c 2.10 a.4.5.32 A, F Homodimer B, D 11 803.23 IdeR 2it0 a 2.60 a.4.5.24 C, D Homodimer E, F 11 1123.8 Phi 434 repressor 2or1 2.50 a.35.1.2 R, L Homodimer A, B 17 1021.78 CgmR 2yvh a 2.50 N/A C, D Homodimer E, F, G, H 10 1056.55 Controller protein 3clc a 2.80 a.35.1.3 C, D Homodimer E, F 14 1002.57 HipB 3dnv 2.68 N/A B, C Homodimer E, T 10 990.24 CprK 3e6c 1.80 a.4.5.4 C, D Homodimer A, B, E, F 12 1059.42 NrtR 3gz6 2.90 N/A A, B Homodimer C, D 15 1845.4 CopG repressor 1b01 2.56 a.43.1.3 A, B Homodimer E, F 5 573.31 RXR-alpha 1by4 2.10 g.39.1.2 A, B Homodimer E, F 8 1031.94 Met repressor 1cma 2.80 a.43.1.5 A, B Homodimer C, D 4 693.13 PhoB 1gxp a 2.50 a.4.6.1 A Monomer C, D 7 739.09 Myb 1h8a a 2.23 a.4.1.3 C Monomer D, E 8 738.59 AML1 Runt domain 1hjc 2.65 b.2.5.6 D Monomer E, F 6 540.76 MtaN 1r8d 2.70 a.6.1.3 A, B Homodimer C, D 8 1338.92 Hard Sigma subunit domain 4 1rio a 2.30 a.4.13.2 H Monomer U, T 6 423.27 Prospero 1xpx 2.80 a.4.1.1 A Monomer C, D 3 325.79 Put3 1zme 2.50 g.38.1.1 C, D Homodimer A, B 5 1211.56 Omega repressor 2bnw 2.45 a.43.1.4 A, B Homodimer E, F 4 519.26 ILF 2c6y 2.40 a.4.5.14 A Monomer C, D 8 814.94 Phi 29 protein p4 2fio 2.70 N/A A, B Homodimer C, D 4 903.33 IRF-2 2irf a 2.20 a.4.5.23 L Monomer C, D 6 668.45 PutA 2rbf 2.25 N/A A, B Homodimer C, D 8 614.12 SoxR 2zhg 2.80 a.6.1.3 A, D Homodimer B, C 6 869.73 Engrailed homeodomain 3hdd a 2.20 a.4.1.1 A Monomer C, D 4 524.73 a Has more than one binding unit b NRBC: number of protein residues having side-chain contacts with DNA bases c BSA: buried surface area in TF-DNA complexes d HT: homotetramer Results Overview of benchmark test cases There are a total of 38 test cases for our TF-DNA docking benchmarks.

Publication Year: 2011

Predicting target DNA sequences of DNA-binding proteins based on unbound structures.

(2012) PLoS One 7

PubMed: 22312425 | PubMedCentral: PMC3270014 | DOI: 10.1371/journal.pone.0030446

PDB Entry name a Protein Seven proteins used as the queries 6CRO RCRO_LAMBD Regulatory protein cro 1MSE MYB_MOUSE Transcriptional activator Myb 1MNN NDT80_YEAST Meiosis-specific transcription factor N... T80 1YRN MATA1_YEAST Mating-type protein A1 1TRO TRPR_ECOLI Trp operon repressor 1RUN CRP_ECOLI Catabolite gene activator 2O61 b NFKB1_HUMAN Nuclear factor NF-kappa-B p105 subunit 13 complexes used for tuning the parameters of the all-atom model 1AAY EGR1_MOUSE Early growth response protein 1 1B8I c UBX_DROME Homeotic protein ultrabithorax EXD_DROME Homeobox protein extradenticle 2DRP TTKB_DROME Protein tramtrack, beta isoform 1FJL PRD_DROME Segmentation protein paired 1GCC ERF1A_ARATH Ethylene-responsive transcription factor 1A 1GXP PHOB_ECOLI Phosphate regulon transcriptional regulatory protein phoB 1J1V DNAA_ECOLI Chromosomal replication initiator protein dnaA 1LMB RPC1_LAMBD Repressor protein CI 1MJ2 METJ_ECOLI Met repressor 2PUC PURR_ECOLI HTH-type transcriptional repressor purR 1R0O USP_DROME Protein ultraspiracle 1YSA GCN4_YEAST General control protein GCN4 1YUI GAGA_DROME Transcription factor GAGA a UniProt entry name.

Publication Year: 2012

Targeted DNA methylation using an artificially bisected M.HhaI fused to zinc fingers.

(2012) PLoS One 7

PubMed: 22984575 | PubMedCentral: PMC3439449 | DOI: 10.1371/journal.pone.0044852

For zinc fingers HS1 and HS2, homology models were constructed using the Rosetta comparative modeling algorithm employing zinc finger Zif268 (1AAY) as the template [25] , [26] .

The orientation of the zinc-fingers and M.HhaI at their respective binding sites was determined by aligning target DNA sequences from M.HhaI/DNA complex (2HR1) and Zif268/DNA complex (1AAY) with the straight B-DNA model.

Publication Year: 2012

Protein-DNA docking with a coarse-grained force field.

(2012) BMC Bioinformatics 13

PubMed: 22966980 | PubMedCentral: PMC3522568 | DOI: 10.1186/1471-2105-13-228

Table 1 Crystallographic protein-DNA complexes (designated by PDB id) with matching experimental binding free energies extracted from ProNIT database PDB Chains ΔG /kcal mol −1 1AAY A/... C −11.5 [ 26 ] 1AZ0 AB/CD −17.4 [ 27 ] 1B72 AB/DE −9.0 [ 28 ] 1BHM AB/CD −11.7 [ 29 ] 1CEZ A/TN −10.8 [ 30 ] 1CMA AB/CD −5.4 [ 31 ] 1D02 AB/CD −8.1 [ 32 ] 1ECR A/BC −15.6 [ 33 ] 1IHF AB/CD −10.3 [ 34 , 35 ] 1PUE E/AB −9.7 [ 36 ] 1QRV A/CD −7.4 [ 37 , 38 ] 1YSA CD/AB −9.5 [ 39 ] 1PUF A/DE −9.2 [ 28 ] 1TRO AC/IJ −12.6 [ 40 - 42 ] 1UBD C/AB −8.5 [ 43 ] A set including crystallographic structures of protein-DNA complexes with corresponding binding affinities provided by Zhang et al. [ 44 ] was considered as an alternative source of data.

Publication Year: 2012

The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks.

(2013) PLoS Comput Biol 9

PubMed: 23300434 | PubMedCentral: PMC3536627 | DOI: 10.1371/journal.pcbi.1002865

(A) Example of in-silico model of DNA-protein complex for the transcription factor EGR1 (PDB:1AAY, originally with sequence 5′-GCGTGGGC-3′ ) bound to the candidate 8-mer 5′-CGT... GTCG-3′ .

Fig. 1A shows the modeled structure of the Egr1 transcription factor bound to the 8-mer 5′-CGTTGTCG-3′ , based on the Egr1-DNA crystal structure (PDB code: 1AAY).

Publication Year: 2013

Prediction of DNA-binding proteins from relational features.

(2012) Proteome Sci 10

PubMed: 23146001 | PubMedCentral: PMC3579737 | DOI: 10.1186/1477-5956-10-66

Example proteins (1A1F and 1AAY) containing one discovered pattern shown for the Zinc-finger proteins’ dataset using the protein viewer software [ 33 ].

Publication Year: 2012

Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease.

(2013) Nucleic Acids Res 41

PubMed: 23125367 | PubMedCentral: PMC3592412 | DOI: 10.1093/nar/gks1043

The duplex DNA was built and modeled together with Zif268 (pdb id; 1aay) and N.φGamma endonuclease domains using program Coot ( 31 ).

Publication Year: 2013

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.

(2014) Nucleic Acids Res 42

PubMed: 25428367 | PubMedCentral: PMC4267649 | DOI: 10.1093/nar/gku1228

The TF2DNA program generates ∼22 mutants per minute, considering a system with ∼1000 atoms (e.g. PDB code: 1AAY – Early Growth Factor 1 TF).

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4330398

Cover: Structure of Cys 2 His 2 zinc finger protein Zif268 complexed with DNA (PDB ID: 1AAY) overlaid on newly discovered zinc finger protein-DNA interaction networks.

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4479991

The crystal structure of zif268, solved via NMR by Pavletich 6 and later improved upon by Elrod-Erickson 51 , is shown in Fig. 1a bound to DNA (PDB ID #1AAY) 52 .

a ) Crystal structure of zif268 (PDB: 1AAY).

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4507475

(B) Crystal structures showing only SIP states for Lys46 in the Antp-DNA complex (PDB 9ANT) 24 and Lys79 in the Egr-1-DNA complex (1AAY).

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

Non-TF/DNA refers to 27 non-transcription factor/DNA complexes (including 1mse, 1tro, 1ca5, 2ezd, 1lcc, 1cjg, 1gcc, 1azp, 1az0, 1b69, 1tf3, 1bhm, 1ecr, 1cw0, 1hcr, 1yui, 1sx9, 7icr, 1qaa, 1jey, 1nk2, ... tau, 5gat, 1qrv, 1a73, 2gat and 1j1v), TF/DNA refers to remaining 21 transcription factor complexes (including 1lmb, 1cma, 1apl, 1par, 1run, 1glu, 1nfk, 1efa, 1mdy, 1tsr, 1ipp, 1ytf, 1vkx, 1oct, 1ihf, 1bc7, 1aay, 1cez, 1yrn, 1ysa and 1b3t).

The protein zif268 (PDB ID 1AAY) consists of three zinc-finger domains, each of which has three amino acids in contact with a DNA site consisting of 3 bp.

Publication Year: 2005