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PDB ID Mentions in PubMed Central Article count: 7

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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Ultra-fast evaluation of protein energies directly from sequence.

(2006) PLoS Comput Biol 2

PubMed: 16789811 | PubMedCentral: PMC1479088 | DOI: 10.1371/journal.pcbi.0020063

To derive a CE describing the Zif268 fold, we defined the backbone using coordinates from the Protein Data Bank (PDB) entry 1ZAA, residues 33–60.

Supporting Information Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb ) accession number for the human PIN1 WW domain is 1PIN and for the murine zinc finger Zif268 is 1ZAA; the SMART database ( http://smart.embl-heidelberg.de ) accession number for the WW domain is SM00456.

Publication Year: 2006


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).

Figure 3 shows ZF helices from three of the five structures (1zaa, 1llm, 1f2i chain K) superimposed with hrZif268 ZF2 helix to further illustrate the degree and nature of docking variation exhibited by different ZF domains and characterized by the corresponding IAS values.

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


ZNF198 stabilizes the LSD1-CoREST-HDAC1 complex on chromatin through its MYM-type zinc fingers.

(2008) PLoS One 3

PubMed: 18806873 | PubMedCentral: PMC2532748 | DOI: 10.1371/journal.pone.0003255

(C) Ribbon drawings of three Krüppel-like zinc fingers bound to DNA (PDB ID: 1ZAA; left) and a MYM-type zinc finger from ZNF237 (PDB ID: 2DAS; right).

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.

A) DNAse I (pdb code: 2DNJ), B) C2H2 zinc finger Zif268 (1ZAA), C) [β]-Zip GCN4 (2DGC), D) Eco RV (1B94), E) I- Mso I (1M5X).

C2H2 zinc finger Zif268 The Zif268 zinc finger transcription factor (pdb code: 1ZAA ( 16 )), shown in Figure 1 B, binds with high affinity and specificity to its operator sequence through a combination of direct contacts to the DNA backbone and major groove.

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 1zaa 1ubd 1g2f 1am9 1gd2 1gu4 1jnm 2dgc 1nkp 1lmb 2or1 1hcr 1ign 1tc3 1bl0 1zs4 2h27 1r71 1pp7 1bc8 1dp7 1f4k.

Publication Year: 2009


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

Methods Starting structure of Zif268, Sp1 protein and DNA The coordinate file of the Zif268-DNA complex was obtained from the RCSB Protein Data Bank [ 29 ] (PDB code: 1ZAA ), and the coordinate of the... bound Zif268 was separated and used as the starting structure.

Publication Year: 2010


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