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PDBsum entry 1aay

Go to PDB code: 
protein dna_rna metals links
Transcription/DNA PDB id
1aay
Jmol
Contents
Protein chain
85 a.a. *
DNA/RNA
Metals
_ZN ×3
Waters ×148
* Residue conservation analysis
PDB id:
1aay
Name: Transcription/DNA
Title: Zif268 zinc finger-DNA complex
Structure: DNA (5'-d( Ap Gp Cp Gp Tp Gp Gp Gp Cp Gp T)-3'). Chain: b. Engineered: yes. DNA (5'-d( Tp Ap Cp Gp Cp Cp Cp Ap Cp Gp C)-3'). Chain: c. Engineered: yes. Protein (zif268 zinc finger peptide). Chain: a. Engineered: yes
Source: Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
1.60Å     R-factor:   0.195     R-free:   0.242
Authors: M.Elrod-Erickson,M.A.Rould,C.O.Pabo
Key ref:
M.Elrod-Erickson et al. (1996). Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure, 4, 1171-1180. PubMed id: 8939742 DOI: 10.1016/S0969-2126(96)00125-6
Date:
18-Jan-97     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08046  (EGR1_MOUSE) -  Early growth response protein 1
Seq:
Struc:
 
Seq:
Struc:
533 a.a.
85 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  

 

 
DOI no: 10.1016/S0969-2126(96)00125-6 Structure 4:1171-1180 (1996)
PubMed id: 8939742  
 
 
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions.
M.Elrod-Erickson, M.A.Rould, L.Nekludova, C.O.Pabo.
 
  ABSTRACT  
 
BACKGROUND: Zinc fingers of the Cys2 His2 class recognize a wide variety of different DNA sequences and are one of the most abundant DNA-binding motifs found in eukaryotes. The previously determined 2.1 A structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-like zinc fingers recognize DNA. RESULTS: We have refined the structure of the Zif268 protein-DNA complex at 1.6 A resolution. Our structure confirms all the basic features of the previous model and allows us to focus on some critical details at the protein-DNA interface. In particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA conformation observed in the Zif268-DNA complex is correlated with finger-finger interactions and the length of the linkers between adjacent fingers. Circular dichroism studies indicate that at least some of the features of this distinctive DNA conformation are induced upon complex formation. CONCLUSIONS: Our 1.6 A structure should provide an excellent framework for analyzing the effects of Zif268 mutations, for modeling related zinc finger-DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overview of the Zif268-DNA complex, showing the side chains that make direct base contacts. The peptide is color-coded by finger: finger one is red, finger two is yellow, and finger three is purple. The DNA is shown in dark blue, and the zinc ions in pale blue.
 
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1171-1180) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20658568 B.Yang, Y.Zhu, Y.Wang, and G.Chen (2011).
Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.
  J Comput Chem, 32, 416-428.  
20047959 A.N.Temiz, P.V.Benos, and C.J.Camacho (2010).
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.
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20010837 A.Sabogal, A.Y.Lyubimov, J.E.Corn, J.M.Berger, and D.C.Rio (2010).
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.
  Nat Struct Mol Biol, 17, 117-123.
PDB code: 3kde
20360772 B.Gonzalez, L.J.Schwimmer, R.P.Fuller, Y.Ye, L.Asawapornmongkol, and C.F.Barbas (2010).
Modular system for the construction of zinc-finger libraries and proteins.
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20623571 C.W.am Ende, H.Y.Meng, M.Ye, A.K.Pandey, and N.J.Zondlo (2010).
Design of lanthanide fingers: compact lanthanide-binding metalloproteins.
  Chembiochem, 11, 1738-1747.  
20594338 D.Davis, and D.Stokoe (2010).
Zinc Finger Nucleases as tools to understand and treat human diseases.
  BMC Med, 8, 42.  
20665475 M.Bueno, N.A.Temiz, and C.J.Camacho (2010).
Novel modulation factor quantifies the role of water molecules in protein interactions.
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20660643 M.Christian, T.Cermak, E.L.Doyle, C.Schmidt, F.Zhang, A.Hummel, A.J.Bogdanove, and D.F.Voytas (2010).
Targeting DNA double-strand breaks with TAL effector nucleases.
  Genetics, 186, 757-761.  
20167128 M.Hatayama, and J.Aruga (2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
  BMC Evol Biol, 10, 53.  
19965883 N.A.Temiz, A.Trapp, O.A.Prokopyev, and C.J.Camacho (2010).
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.
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20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
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20160705 T.J.Cradick, K.Keck, S.Bradshaw, A.C.Jamieson, and A.P.McCaffrey (2010).
Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs.
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19574296 A.M.Van der Sloot, C.Kiel, L.Serrano, and F.Stricher (2009).
Protein design in biological networks: from manipulating the input to modifying the output.
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19319441 A.Nomura, and A.Okamoto (2009).
Photoresponsive tandem zinc finger peptide.
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19008249 A.V.Persikov, R.Osada, and M.Singh (2009).
Predicting DNA recognition by Cys2His2 zinc finger proteins.
  Bioinformatics, 25, 22-29.  
19002164 E.M.Händel, S.Alwin, and T.Cathomen (2009).
Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity.
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19389725 J.Ashworth, and D.Baker (2009).
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
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19056825 J.D.Sander, P.Zaback, J.K.Joung, D.F.Voytas, and D.Dobbs (2009).
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.
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19198653 J.E.Foley, J.R.Yeh, M.L.Maeder, D.Reyon, J.D.Sander, R.T.Peterson, and J.K.Joung (2009).
Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN).
  PLoS ONE, 4, e4348.  
20041164 J.H.Thomas, R.O.Emerson, and J.Shendure (2009).
Extraordinary molecular evolution in the PRDM9 fertility gene.
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19186211 K.Su, D.Wang, J.Ye, Y.C.Kim, and S.A.Chow (2009).
Site-specific integration of retroviral DNA in human cells using fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc-finger protein E2C.
  Methods, 47, 269-276.  
19798082 M.L.Maeder, S.Thibodeau-Beganny, J.D.Sander, D.F.Voytas, and J.K.Joung (2009).
Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays.
  Nat Protoc, 4, 1471-1501.  
19429892 N.A.Temiz, and C.J.Camacho (2009).
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.
  Nucleic Acids Res, 37, 4076-4088.  
19363034 P.J.Dittmer, J.G.Miranda, J.A.Gorski, and A.E.Palmer (2009).
Genetically encoded sensors to elucidate spatial distribution of cellular zinc.
  J Biol Chem, 284, 16289-16297.  
19701937 S.Sakkhachornphop, S.Jiranusornkul, K.Kodchakorn, S.Nangola, T.Sirisanthana, and C.Tayapiwatana (2009).
Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions.
  Protein Sci, 18, 2219-2230.  
19394375 T.Sera (2009).
Zinc-finger-based artificial transcription factors and their applications.
  Adv Drug Deliv Rev, 61, 513-526.  
18487511 B.K.Singleton, N.M.Burton, C.Green, R.L.Brady, and D.J.Anstee (2008).
Mutations in EKLF/KLF1 form the molecular basis of the rare blood group In(Lu) phenotype.
  Blood, 112, 2081-2088.  
18586699 J.Liu, and G.D.Stormo (2008).
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
  Bioinformatics, 24, 1850-1857.  
18657511 M.L.Maeder, S.Thibodeau-Beganny, A.Osiak, D.A.Wright, R.M.Anthony, M.Eichtinger, T.Jiang, J.E.Foley, R.J.Winfrey, J.A.Townsend, E.Unger-Wallace, J.D.Sander, F.Müller-Lerch, F.Fu, J.Pearlberg, C.Göbel, J.P.Dassie, S.M.Pruett-Miller, M.H.Porteus, D.C.Sgroi, A.J.Iafrate, D.Dobbs, P.B.McCray, T.Cathomen, D.F.Voytas, and J.K.Joung (2008).
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.
  Mol Cell, 31, 294-301.  
18545224 T.Cathomen, and J.K.Joung (2008).
Zinc-finger nucleases: the next generation emerges.
  Mol Ther, 16, 1200-1207.  
18026168 T.I.Cornu, S.Thibodeau-Beganny, E.Guhl, S.Alwin, M.Eichtinger, J.Joung, and T.Cathomen (2008).
DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.
  Mol Ther, 16, 352-358.  
18410495 Y.Zheng, J.Kief, K.Auffarth, J.W.Farfsing, M.Mahlert, F.Nieto, and C.W.Basse (2008).
The Ustilago maydis Cys2His2-type zinc finger transcription factor Mzr1 regulates fungal gene expression during the biotrophic growth stage.
  Mol Microbiol, 68, 1450-1470.  
17335000 D.Lu, and A.Klug (2007).
Invariance of the zinc finger module: a comparison of the free structure with those in nucleic-acid complexes.
  Proteins, 67, 508-512.
PDB code: 2j7j
17214883 F.Spyrakis, P.Cozzini, C.Bertoli, A.Marabotti, G.E.Kellogg, and A.Mozzarelli (2007).
Energetics of the protein-DNA-water interaction.
  BMC Struct Biol, 7, 4.  
17603475 J.C.Miller, M.C.Holmes, J.Wang, D.Y.Guschin, Y.L.Lee, I.Rupniewski, C.M.Beausejour, A.J.Waite, N.S.Wang, K.A.Kim, P.D.Gregory, C.O.Pabo, and E.J.Rebar (2007).
An improved zinc-finger nuclease architecture for highly specific genome editing.
  Nat Biotechnol, 25, 778-785.  
17264128 T.W.Siggers, and B.Honig (2007).
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
  Nucleic Acids Res, 35, 1085-1097.  
17537811 X.Meng, S.Thibodeau-Beganny, T.Jiang, J.K.Joung, and S.A.Wolfe (2007).
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method.
  Nucleic Acids Res, 35, e81.  
16834537 A.Beltran, Y.Liu, S.Parikh, B.Temple, and P.Blancafort (2006).
Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions.
  Assay Drug Dev Technol, 4, 317-331.  
16533044 A.T.Ooi, C.I.Stains, I.Ghosh, and D.J.Segal (2006).
Sequence-enabled reassembly of beta-lactamase (SEER-LAC): a sensitive method for the detection of double-stranded DNA.
  Biochemistry, 45, 3620-3625.  
16685715 B.D.Allen, and S.L.Mayo (2006).
Dramatic performance enhancements for the FASTER optimization algorithm.
  J Comput Chem, 27, 1071-1075.  
16467376 K.S.Moorefield, H.Yin, T.D.Nichols, C.Cathcart, S.O.Simmons, and J.M.Horowitz (2006).
Sp2 localizes to subnuclear foci associated with the nuclear matrix.
  Mol Biol Cell, 17, 1711-1722.  
16891881 N.S.Buttar, M.E.Fernandez-Zapico, and R.Urrutia (2006).
Key role of Krüppel-like factor proteins in pancreatic cancer and other gastrointestinal neoplasias.
  Curr Opin Gastroenterol, 22, 505-511.  
16906878 R.G.Endres, and N.S.Wingreen (2006).
Weight matrices for protein-DNA binding sites from a single co-crystal structure.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 061921.  
16445281 S.Ladame, J.A.Schouten, J.Roldan, J.E.Redman, S.Neidle, and S.Balasubramanian (2006).
Exploring the recognition of quadruplex DNA by an engineered Cys2-His2 zinc finger protein.
  Biochemistry, 45, 1393-1399.  
16892470 Y.Singh, G.T.Dolphin, J.Razkin, and P.Dumy (2006).
Synthetic Peptide templates for molecular recognition: recent advances and applications.
  Chembiochem, 7, 1298-1314.  
16107335 B.Dreier, R.P.Fuller, D.J.Segal, C.V.Lund, P.Blancafort, A.Huber, B.Koksch, and C.F.Barbas (2005).
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors.
  J Biol Chem, 280, 35588-35597.  
16121397 D.Lejeune, N.Delsaux, B.Charloteaux, A.Thomas, and R.Brasseur (2005).
Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure.
  Proteins, 61, 258-271.  
16014175 J.Liu, and G.D.Stormo (2005).
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
  BMC Bioinformatics, 6, 176.  
15545275 J.Mostecki, B.M.Showalter, and P.B.Rothman (2005).
Early growth response-1 regulates lipopolysaccharide-induced suppressor of cytokine signaling-1 transcription.
  J Biol Chem, 280, 2596-2605.  
15713659 K.L.Brady, and D.R.Setzer (2005).
Is there a dynamic DNA-protein interface in the transcription factor IIIA-5 S rRNA gene complex?
  J Biol Chem, 280, 16115-16124.  
15888446 K.L.Brady, S.N.Ponnampalam, M.J.Bumbulis, and D.R.Setzer (2005).
Mutations in TFIIIA that increase stability of the TFIIIA-5 S rRNA gene complex: unusual effects on the kinetics of complex assembly and dissociation.
  J Biol Chem, 280, 26743-26750.  
15613596 G.Paillard, C.Deremble, and R.Lavery (2004).
Looking into DNA recognition: zinc finger binding specificity.
  Nucleic Acids Res, 32, 6673-6682.  
14725771 G.Paillard, and R.Lavery (2004).
Analyzing protein-DNA recognition mechanisms.
  Structure, 12, 113-122.  
15557258 M.J.Lachenmann, J.E.Ladbury, X.Qian, K.Huang, R.Singh, and M.A.Weiss (2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
  Protein Sci, 13, 3115-3126.
PDB code: 1xrz
15340913 R.G.Endres, T.C.Schulthess, and N.S.Wingreen (2004).
Toward an atomistic model for predicting transcription-factor binding sites.
  Proteins, 57, 262-268.  
14722285 W.Tan, K.Zhu, D.J.Segal, C.F.Barbas, and S.A.Chow (2004).
Fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc finger protein E2C direct integration of viral DNA into specific sites.
  J Virol, 78, 1301-1313.  
14610091 X.Chen, B.Zhang, P.M.Harmon, W.Schaffner, D.O.Peterson, and D.P.Giedroc (2004).
A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo.
  J Biol Chem, 279, 4515-4522.  
12837939 A.Akopian, J.He, M.R.Boocock, and W.M.Stark (2003).
Chimeric recombinases with designed DNA sequence recognition.
  Proc Natl Acad Sci U S A, 100, 8688-8691.  
12616630 C.Isernia, E.Bucci, M.Leone, L.Zaccaro, P.Di Lello, G.Digilio, S.Esposito, M.Saviano, B.Di Blasio, C.Pedone, P.V.Pedone, and R.Fattorusso (2003).
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
  Chembiochem, 4, 171-180.
PDB code: 1njq
12898671 C.S.Yeh, F.M.Chen, J.Y.Wang, T.L.Cheng, M.J.Hwang, and W.S.Tzou (2003).
Directional shape complementarity at the protein-DNA interface.
  J Mol Recognit, 16, 213-222.  
12804117 H.R.Chrisman, and D.J.Tindall (2003).
Identification and characterization of a consensus DNA binding element for the zinc finger transcription factor TIEG/EGRalpha.
  DNA Cell Biol, 22, 187-199.  
12620113 J.Kaczynski, T.Cook, and R.Urrutia (2003).
Sp1- and Krüppel-like transcription factors.
  Genome Biol, 4, 206.  
12876317 K.Koscielska-Kasprzak, and J.Otlewski (2003).
Amyloid-forming peptides selected proteolytically from phage display library.
  Protein Sci, 12, 1675-1685.  
12592412 P.Blancafort, L.Magnenat, and C.F.Barbas (2003).
Scanning the human genome with combinatorial transcription factor libraries.
  Nat Biotechnol, 21, 269-274.  
14621985 S.A.Wolfe, R.A.Grant, and C.O.Pabo (2003).
Structure of a designed dimeric zinc finger protein bound to DNA.
  Biochemistry, 42, 13401-13409.
PDB code: 1llm
12682016 S.X.Cohen, M.Moulin, S.Hashemolhosseini, K.Kilian, M.Wegner, and C.W.Müller (2003).
Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition.
  EMBO J, 22, 1835-1845.
PDB code: 1odh
11844803 K.Pandya, and T.M.Townes (2002).
Basic residues within the Kruppel zinc finger DNA binding domains are the critical nuclear localization determinants of EKLF/KLF-1.
  J Biol Chem, 277, 16304-16312.  
12001270 P.V.Benos, A.S.Lapedes, and G.D.Stormo (2002).
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .
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12384591 P.V.Benos, M.L.Bulyk, and G.D.Stormo (2002).
Additivity in protein-DNA interactions: how good an approximation is it?
  Nucleic Acids Res, 30, 4442-4451.  
11726671 Q.Liu, Z.Xia, X.Zhong, and C.C.Case (2002).
Validated zinc finger protein designs for all 16 GNN DNA triplet targets.
  J Biol Chem, 277, 3850-3856.  
12271125 X.Guan, J.Stege, M.Kim, Z.Dahmani, N.Fan, P.Heifetz, C.F.Barbas, and S.P.Briggs (2002).
Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors.
  Proc Natl Acad Sci U S A, 99, 13296-13301.  
11395410 C.O.Pabo, E.Peisach, and R.A.Grant (2001).
Design and selection of novel Cys2His2 zinc finger proteins.
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11849947 D.J.Segal, and C.F.Barbas (2001).
Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins.
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11554446 D.P.Giedroc, X.Chen, and J.L.Apuy (2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
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11433278 M.Isalan, A.Klug, and Y.Choo (2001).
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.
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11170401 M.Isalan, S.D.Patel, S.Balasubramanian, and Y.Choo (2001).
Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation.
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11404456 M.L.Bulyk, X.Huang, Y.Choo, and G.M.Church (2001).
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.
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11171969 M.Moore, A.Klug, and Y.Choo (2001).
Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units.
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11258905 M.Nagaoka, T.Kaji, M.Imanishi, Y.Hori, W.Nomura, and Y.Sugiura (2001).
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11812820 M.Nagaoka, Y.Shiraishi, and Y.Sugiura (2001).
Selected base sequence outside the target binding site of zinc finger protein Sp1.
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11410653 T.K.Man, and G.D.Stormo (2001).
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.
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11327841 Y.Uno, K.Matsushita, M.Nagaoka, and Y.Sugiura (2001).
Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition.
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10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
11121477 A.R.McNamara, and K.G.Ford (2000).
A novel four zinc-finger protein targeted against p190(BcrAbl) fusion oncogene cDNA: utilisation of zinc-finger recognition codes.
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11137451 D.T.Dang, J.Pevsner, and V.W.Yang (2000).
The biology of the mammalian Krüppel-like family of transcription factors.
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11050227 J.H.Laity, H.J.Dyson, and P.E.Wright (2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
  Proc Natl Acad Sci U S A, 97, 11932-11935.  
10757987 M.Imanishi, Y.Hori, M.Nagaoka, and Y.Sugiura (2000).
DNA-bending finger: artificial design of 6-zinc finger peptides with polyglycine linker and induction of DNA bending.
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10773080 M.Schaub, A.Krol, and P.Carbon (2000).
Structural organization of Staf-DNA complexes.
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10903945 S.A.Wolfe, E.I.Ramm, and C.O.Pabo (2000).
Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers.
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10940247 S.A.Wolfe, L.Nekludova, and C.O.Pabo (2000).
DNA recognition by Cys2His2 zinc finger proteins.
  Annu Rev Biophys Biomol Struct, 29, 183-212.  
10637336 S.Lee, and M.D.Garfinkel (2000).
Characterization of Drosophila OVO protein DNA binding specificity using random DNA oligomer selection suggests zinc finger degeneration.
  Nucleic Acids Res, 28, 826-834.  
10981627 Y.Choo, and M.Isalan (2000).
Advances in zinc finger engineering.
  Curr Opin Struct Biol, 10, 411-416.  
10077584 D.J.Segal, B.Dreier, R.R.Beerli, and C.F.Barbas (1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
  Proc Natl Acad Sci U S A, 96, 2758-2763.  
10685047 G.S.Beligere, and P.E.Dawson (1999).
Synthesis of a three zinc finger protein, Zif268, by native chemical ligation.
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10517155 G.Tuchscherer, D.Grell, M.Mathieu, and M.Mutter (1999).
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Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding.
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PDB code: 6pax
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
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10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
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PDB codes: 1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l
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Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
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Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
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Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
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PDB code: 1tf6
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Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1.
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9546210 Y.Choo, and J.W.Schwabe (1998).
All wrapped up.
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Recognition of DNA methylation by zinc fingers.
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End effects in DNA recognition by zinc finger arrays.
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Three-dimensional domain duplication, swapping and stealing.
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Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy.
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Synergy between adjacent zinc fingers in sequence-specific DNA recognition.
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NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
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Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
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9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
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Physical basis of a protein-DNA recognition code.
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