PDBsum entry 1aay

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protein dna_rna metals links
Transcription/DNA PDB id
Protein chain
85 a.a. *
_ZN ×3
Waters ×148
* Residue conservation analysis
PDB id:
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)
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
18-Jan-97     Release date:   21-Apr-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08046  (EGR1_MOUSE) -  Early growth response protein 1
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.
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).
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PDB code: 3kde
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PDB code: 2j7j
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15545275 J.Mostecki, B.M.Showalter, and P.B.Rothman (2005).
Early growth response-1 regulates lipopolysaccharide-induced suppressor of cytokine signaling-1 transcription.
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Is there a dynamic DNA-protein interface in the transcription factor IIIA-5 S rRNA gene complex?
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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.
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15613596 G.Paillard, C.Deremble, and R.Lavery (2004).
Looking into DNA recognition: zinc finger binding specificity.
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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).
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NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
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PDB code: 1njq
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Directional shape complementarity at the protein-DNA interface.
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Identification and characterization of a consensus DNA binding element for the zinc finger transcription factor TIEG/EGRalpha.
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Structure of a designed dimeric zinc finger protein bound to DNA.
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PDB code: 1llm
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PDB code: 1odh
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PDB code: 1ec5
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Structural organization of Staf-DNA complexes.
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DNA recognition by Cys2His2 zinc finger proteins.
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Advances in zinc finger engineering.
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Extending the concept of template-assembled synthetic proteins.
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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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10383437 M.Elrod-Erickson, and C.O.Pabo (1999).
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10446199 M.Schaub, A.Krol, and P.Carbon (1999).
Flexible zinc finger requirement for binding of the transcriptional activator staf to U6 small nuclear RNA and tRNA(Sec) promoters.
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10455183 M.Schaub, E.Myslinski, A.Krol, and P.Carbon (1999).
Maximization of selenocysteine tRNA and U6 small nuclear RNA transcriptional activation achieved by flexible utilization of a Staf zinc finger.
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10454592 S.Philipsen, and G.Suske (1999).
A tale of three fingers: the family of mammalian Sp/XKLF transcription factors.
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De novo design and structural characterization of proteins and metalloproteins.
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9705341 E.Myslinski, A.Krol, and P.Carbon (1998).
ZNF76 and ZNF143 are two human homologs of the transcriptional activator Staf.
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Regulation of zinc homeostasis in yeast by binding of the ZAP1 transcriptional activator to zinc-responsive promoter elements.
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Analysis of zinc binding sites in protein crystal structures.
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9467467 J.L.Pomerantz, S.A.Wolfe, and C.O.Pabo (1998).
Structure-based design of a dimeric zinc finger protein.
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9501172 J.S.Kim, and C.O.Pabo (1998).
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PDB codes: 1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l
9724513 M.Isalan, A.Klug, and Y.Choo (1998).
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
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9578568 M.Yokono, N.Saegusa, K.Matsushita, and Y.Sugiura (1998).
Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
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Regulation of POU genes by castor and hunchback establishes layered compartments in the Drosophila CNS.
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Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks.
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9501194 R.T.Nolte, R.M.Conlin, S.C.Harrison, and R.S.Brown (1998).
Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
  Proc Natl Acad Sci U S A, 95, 2938-2943.
PDB code: 1tf6
9485332 T.B.Hamilton, F.Borel, and P.J.Romaniuk (1998).
Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1.
  Biochemistry, 37, 2051-2058.  
9546210 Y.Choo, and J.W.Schwabe (1998).
All wrapped up.
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9546213 Y.Choo (1998).
Recognition of DNA methylation by zinc fingers.
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9421515 Y.Choo (1998).
End effects in DNA recognition by zinc finger arrays.
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9580679 Y.Mandel-Gutfreund, and H.Margalit (1998).
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.
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9005850 H.A.Greisman, and C.O.Pabo (1997).
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
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9204285 J.Heringa, and W.R.Taylor (1997).
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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9159121 M.Isalan, Y.Choo, and A.Klug (1997).
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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9369471 M.Schmiedeskamp, and R.E.Klevit (1997).
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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9032060 Y.Choo, and A.Klug (1997).
Physical basis of a protein-DNA recognition code.
  Curr Opin Struct Biol, 7, 117-125.  
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