PDBsum entry 4znf

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Zinc finger DNA binding domain PDB id
Protein chain
30 a.a. *
* Residue conservation analysis
PDB id:
Name: Zinc finger DNA binding domain
Title: High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution
Structure: Zinc finger. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 41 models
Authors: A.M.Gronenborn,G.M.Clore,J.G.Omichinski
Key ref:
J.G.Omichinski et al. (1990). High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution. Biochemistry, 29, 9324-9334. PubMed id: 2248949 DOI: 10.1021/bi00492a004
09-Jul-90     Release date:   15-Jan-92    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P15822  (ZEP1_HUMAN) -  Zinc finger protein 40
2718 a.a.
30 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

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


DOI no: 10.1021/bi00492a004 Biochemistry 29:9324-9334 (1990)
PubMed id: 2248949  
High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution.
J.G.Omichinski, G.M.Clore, E.Appella, K.Sakaguchi, A.M.Gronenborn.
The three-dimensional structure of a 30-residue synthetic peptide containing the carboxy-terminal "zinc finger" motif of a human enhancer binding protein has been determined by two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on 487 approximate interproton distance and 63 torsion angle (phi, psi, and chi 1) restraints. A total of 40 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 29 and 30 which are ill-defined) is 0.4 A for the backbone atoms, 0.8 A for all atoms, and 0.41 A for all atoms excluding the lysine and arginine side chains, which are disordered. The solution structure of the zinc finger consists of two irregular antiparallel beta-strands connected by an atypical turn (residues 3-12) and a classical alpha-helix (residues 14-24). The zinc is tetrahedrally coordinated to the sulfur atoms of two cysteines (Cys-5 and Cys-8) and to the N epsilon 2 atoms of two histidines (His-21 and His-27). The two cysteine residues are located in the turn connecting the two beta-strands (residues 5-8); one of the histidine ligands (His-21) is in the alpha-helix, while the second histidine (His-27) is at the end of a looplike structure (formed by the end of the alpha-helix and a turn). The general architecture is qualitatively similar to two previously determined low-resolution Cys2-His2 zinc finger structures, although distinct differences can be observed in the beta-strands and turn and in the region around the two histidines coordinated to zinc. Comparison of the overall polypeptide fold of the enhancer binding protein zinc finger with known structures in the crystallographic data base reveals a striking similarity to one region (residues 23-44) of the X-ray structure of proteinase inhibitor domain III of Japanese quail ovomucoid [Papamokos, E., Weber, E., Bode, W., Huber, R., Empie, M. W., Kato, I., & Laskowski, M. (1982) J. Mol. Biol. 158, 515-537], which could be superimposed with a backbone atomic rms difference of 0.95 A on residues 3-25 (excluding residue 6) of the zinc finger from the enhancer binding protein. The presence of structural homology between two proteins of very different function may indicate that the so-called zinc finger motif is not unique for a class of DNA binding proteins but may represent a general folding motif found in a variety of proteins irrespective of their function.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.
  Nucleic Acids Res, 38, 2134-2144.  
18359862 M.C.Bauer, H.Nilsson, E.Thulin, B.Frohm, J.Malm, and S.Linse (2008).
Zn2+ binding to human calbindin D(28k) and the role of histidine residues.
  Protein Sci, 17, 760-767.  
18287285 P.L.Hayes, B.L.Lytle, B.F.Volkman, and F.C.Peterson (2008).
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein.
  Protein Sci, 17, 571-576.
PDB code: 1zr9
17786587 G.N.Phillips, B.G.Fox, J.L.Markley, B.F.Volkman, E.Bae, E.Bitto, C.A.Bingman, R.O.Frederick, J.G.McCoy, B.L.Lytle, B.S.Pierce, J.Song, and S.N.Twigger (2007).
Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.
  J Struct Funct Genomics, 8, 73-84.  
16415022 N.J.Baxter, A.Roetzer, H.D.Liebig, S.E.Sedelnikova, A.M.Hounslow, T.Skern, and J.P.Waltho (2006).
Structure and dynamics of coxsackievirus B4 2A proteinase, an enyzme involved in the etiology of heart disease.
  J Virol, 80, 1451-1462.
PDB code: 1z8r
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
  11045620 H.T.Chen, P.Legault, J.Glushka, J.G.Omichinski, and R.A.Scott (2000).
Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.
  Protein Sci, 9, 1743-1752.
PDB code: 1dl6
10079767 H.Yamamoto, J.Sejbal, E.York, J.M.Stewart, L.D.Possani, and G.Kotovych (1999).
An nmr conformational analysis of a synthetic peptide Cn2(1-15)NH2-S-S-acetyl-Cn2(52-66)NH2 from the New World Centruroides noxius 2 (Cn2) scorpion toxin: comparison of the structure with those of the Centruroides scorpion toxins.
  Biopolymers, 49, 277-286.  
9857076 S.C.Mateer, S.A.Fedorov, and M.C.Mumby (1998).
Identification of structural elements involved in the interaction of simian virus 40 small tumor antigen with protein phosphatase 2A.
  J Biol Chem, 273, 35339-35346.  
9033593 J.G.Omichinski, P.V.Pedone, G.Felsenfeld, A.M.Gronenborn, and G.M.Clore (1997).
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
  Nat Struct Biol, 4, 122-132.
PDB codes: 1yui 1yuj
9228950 M.Cai, R.Zheng, M.Caffrey, R.Craigie, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the N-terminal zinc binding domain of HIV-1 integrase.
  Nat Struct Biol, 4, 567-577.
PDB codes: 1wja 1wjb 1wjc 1wjd
8917505 A.C.Jamieson, H.Wang, and S.H.Kim (1996).
A zinc finger directory for high-affinity DNA recognition.
  Proc Natl Acad Sci U S A, 93, 12834-12839.  
8610125 P.V.Pedone, R.Ghirlando, G.M.Clore, A.M.Gronenborn, G.Felsenfeld, and J.G.Omichinski (1996).
The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.
  Proc Natl Acad Sci U S A, 93, 2822-2826.  
8736557 R.N.Dutnall, D.Neuhaus, and D.Rhodes (1996).
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
  Structure, 4, 599-611.
PDB code: 1ncs
8692697 S.J.McBryant, B.Gedulin, K.R.Clemens, P.E.Wright, and J.M.Gottesfeld (1996).
Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA.
  Nucleic Acids Res, 24, 2567-2574.  
7831288 H.Wu, W.P.Yang, and C.F.Barbas (1995).
Building zinc fingers by selection: toward a therapeutic application.
  Proc Natl Acad Sci U S A, 92, 344-348.  
7797503 U.C.Marx, S.Austermann, P.Bayer, K.Adermann, A.Ejchart, H.Sticht, S.Walter, F.X.Schmid, R.Jaenicke, and W.G.Forssmann (1995).
Structure of human parathyroid hormone 1-37 in solution.
  J Biol Chem, 270, 15194-15202.
PDB code: 1hph
8092710 B.E.Bernstein, R.C.Hoffman, and R.E.Klevit (1994).
Sequence-specific DNA recognition by Cys2, His2 zinc fingers.
  Ann N Y Acad Sci, 726, 92.  
  7527339 H.Terasawa, D.Kohda, H.Hatanaka, K.Nagata, N.Higashihashi, H.Fujiwara, K.Sakano, and F.Inagaki (1994).
Solution structure of human insulin-like growth factor II; recognition sites for receptors and binding proteins.
  EMBO J, 13, 5590-5597.  
7984421 M.L.Nedved, and G.R.Moe (1994).
Cooperative, non-specific binding of a zinc finger peptide to DNA.
  Nucleic Acids Res, 22, 4705-4711.  
8078776 M.Suzuki, M.Gerstein, and N.Yagi (1994).
Stereochemical basis of DNA recognition by Zn fingers.
  Nucleic Acids Res, 22, 3397-3405.  
  8401216 B.A.Krizek, L.E.Zawadzke, and J.M.Berg (1993).
Independence of metal binding between tandem Cys2His2 zinc finger domains.
  Protein Sci, 2, 1313-1319.  
  8318898 M.J.Sutcliffe (1993).
Representing an ensemble of NMR-derived protein structures by a single structure.
  Protein Sci, 2, 936-944.  
8272423 M.W.MacArthur, and J.M.Thornton (1993).
Conformational analysis of protein structures derived from NMR data.
  Proteins, 17, 232-251.  
  8318900 R.C.Hoffman, S.J.Horvath, and R.E.Klevit (1993).
Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
  Protein Sci, 2, 951-965.
PDB codes: 1ard 1are 1arf
  1569931 A.D.Keller, and T.Maniatis (1992).
Only two of the five zinc fingers of the eukaryotic transcriptional repressor PRDI-BF1 are required for sequence-specific DNA binding.
  Mol Cell Biol, 12, 1940-1949.  
  1425585 G.H.Jacobs (1992).
Determination of the base recognition positions of zinc fingers from sequence analysis.
  EMBO J, 11, 4507-4517.  
1454785 J.M.Berg (1992).
Sp1 and the subfamily of zinc finger proteins with guanine-rich binding sites.
  Proc Natl Acad Sci U S A, 89, 11109-11110.  
1508708 J.Nardelli, T.Gibson, and P.Charnay (1992).
Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis.
  Nucleic Acids Res, 20, 4137-4144.  
1408784 L.Fairall, and D.Rhodes (1992).
A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex.
  Nucleic Acids Res, 20, 4727-4731.  
  1304355 M.F.Summers, L.E.Henderson, M.R.Chance, J.W.Bess, T.L.South, P.R.Blake, I.Sagi, G.Perez-Alvarado, R.C.Sowder, and D.R.Hare (1992).
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.
  Protein Sci, 1, 563-574.
PDB code: 1aaf
1324755 M.S.Lee, A.G.Palmer, and P.E.Wright (1992).
Relationship between 1H and 13C NMR chemical shifts and the secondary and tertiary structure of a zinc finger peptide.
  J Biomol NMR, 2, 307-322.  
1511742 M.S.Lee, R.J.Mortishire-Smith, and P.E.Wright (1992).
The zinc finger motif. Conservation of chemical shifts and correlation with structure.
  FEBS Lett, 309, 29-32.  
1570325 N.A.Woychik, and R.A.Young (1992).
Genes encoding transcription factor IIIA and the RNA polymerase common subunit RPB6 are divergently transcribed in Saccharomyces cerevisiae.
  Proc Natl Acad Sci U S A, 89, 3999-4003.  
1594580 S.F.Michael, V.J.Kilfoil, M.H.Schmidt, B.T.Amann, and J.M.Berg (1992).
Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide.
  Proc Natl Acad Sci U S A, 89, 4796-4800.  
1668718 G.M.Clore, A.Bax, and A.M.Gronenborn (1991).
Stereospecific assignment of beta-methylene protons in larger proteins using 3D 15N-separated Hartmann-Hahn and 13C-separated rotating frame Overhauser spectroscopy.
  J Biomol NMR, 1, 13-22.  
1959614 J.G.Omichinski, G.M.Clore, K.Sakaguchi, E.Appella, and A.M.Gronenborn (1991).
Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy.
  FEBS Lett, 292, 25-30.
PDB code: 1ncp
1924304 M.Kochoyan, H.T.Keutmann, and M.A.Weiss (1991).
Architectural rules of the zinc-finger motif: comparative two-dimensional NMR studies of native and "aromatic-swap" domains define a "weakly polar switch".
  Proc Natl Acad Sci U S A, 88, 8455-8459.  
1924382 S.K.Thukral, M.L.Morrison, and E.T.Young (1991).
Alanine scanning site-directed mutagenesis of the zinc fingers of transcription factor ADR1: residues that contact DNA and that transactivate.
  Proc Natl Acad Sci U S A, 88, 9188-9192.  
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