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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.
Publication Year: 2007
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
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
MATERIALS AND METHODS Structural data The following high-resolution crystal structures of protein–DNA complexes were modeled: Helical transcription factors: 1ig7 1k61 1puf 2hdd 1w0u 1e3o 2d5v ... zaa 1ubd 1g2f 1am9 1gd2 1gu4 1jnm 2dgc 1nkp 1lmb 2or1 1hcr 1ign 1tc3 1bl0 1zs4 2h27 1r71 1pp7 1bc8 1dp7 1f4k.
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
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
(2010) BMC Evol Biol 10
PubMed: 20167128 | PubMedCentral: PMC2837044 | DOI: 10.1186/1471-2148-10-53
Furthermore, the structure of GLI, ZIC3, and Zap1 tCWCH2 domains, in which the two adjacent ZFs form a single globular structure [ 7 , 13 , 47 ], is clearly different from the structure of the DNA-bin... ing C2H2 ZF domain where each globular ZF unit wraps around the major groove of the DNA [ 7 - 11 , 64 ] (PDBID: GLI, 2GLI ; YY1, 1UBD ; WT1, 2RPT ; Zif268, 1MEY , 1P47 ; TFIIIA; 1TF3 ).
Publication Year: 2010
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
(2010) BMC Bioinformatics 11
PubMed: 20565873 | PubMedCentral: PMC2905368 | DOI: 10.1186/1471-2105-11-334
Complex modeling of other test cases, YY1, WT1 and Aart We also extended this method to analyze other classical Cys 2 His 2 zinc-finger proteins with known crystal structures, YY1 (PDB code: 1UBD ), W... 1 (PDB code: 2JP9 ) and Aart (PDB code: 2I13 ).
Conservation of the three-dimensional structure in non-homologous or unrelated proteins.
(2012) Hum Genomics 6
PubMed: 23244440 | PubMedCentral: PMC3500211 | DOI: 10.1186/1479-7364-6-10
YY1 (PDB: 1UBD) [ 73 ] is a protein with four Zn fingers and is structurally similar to kruppel-like factor 3 (PDB: 1U85), which contains a Zn finger with tryptophan as shown in the fourth example.
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.
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
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