PDBsum entry 1tf6

Transcription/DNA

PDB id: 1tf6

Contents

Protein chains

179 a.a. *

DNA/RNA

Metals

_ZN ×12

* Residue conservation analysis

PDB id:

1tf6

Name:

Transcription/DNA

Title:

Co-crystal structure of xenopus tfiiia zinc finger domain bound to the 5s ribosomal RNA gene internal control region

Structure:

DNA (5'- d( Ap Cp Gp Gp Gp Cp Cp Tp Gp Gp Tp Tp Ap Gp Tp Ap C p Cp Tp Gp Gp Ap Tp Gp Gp Gp Ap Gp Ap Cp C)-3'). Chain: b, e. Fragment: internal promoter region. Synonym: 5s ribosomal RNA gene. Engineered: yes. DNA (5'- d( Tp Gp Gp Tp Cp Tp Cp Cp Cp Ap Tp Cp Cp Ap Gp Gp T

Source:

Synthetic: yes. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Organ: ovary. Cell: oocyte. Organelle: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PDB file)

Resolution:

3.10Å R-factor: 0.308 R-free: 0.363

Authors:

R.T.Nolte,R.M.Conlin,S.C.Harrison,R.S.Brown

Key ref:

R.T.Nolte et al. (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. PubMed id: 9501194 DOI: 10.1073/pnas.95.6.2938

Date:

02-Mar-98 Release date: 10-Jul-98

Protein chains

P03001  (TF3A_XENLA) -  Transcription factor IIIA from Xenopus laevis

Seq: 366 a.a.

Struc: 179 a.a.

DNA/RNA chains

A-C-G-G-G-C-C-T-G-G-T-T-A-G-T-A-C-C-T-G-G-A-T-G-G-G-A-G-A-C-C 31 bases

T-G-G-T-C-T-C-C-C-A-T-C-C-A-G-G-T-A-C-T-A-A-C-C-A-G-G-C-C-C-G 31 bases

A-C-G-G-G-C-C-T-G-G-T-T-A-G-T-A-C-C-T-G-G-A-T-G-G-G-A-G-A-C-C 31 bases

T-G-G-T-C-T-C-C-C-A-T-C-C-A-G-G-T-A-C-T-A-A-C-C-A-G-G-C-C-C-G 31 bases

DOI no: 10.1073/pnas.95.6.2938

Proc Natl Acad Sci U S A 95:2938-2943 (1998)

PubMed id: 9501194

Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.

R.T.Nolte, R.M.Conlin, S.C.Harrison, R.S.Brown.

ABSTRACT

The crystal structure of the six NH2-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound with 31 bp of the 5S rRNA gene promoter has been determined at 3.1 A resolution. Individual zinc fingers are positioned differently in the major groove and across the minor groove of DNA to span the entire length of the duplex. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove.

Selected figure(s)

Figure 1.
Fig. 1. Sequences of the DNA and protein used for crystallization. (A) Pol III elements within the X. laevis oocyte 5S rRNA ICR (base^ pairs +43 to +97) are shown boxed. The 31-bp duplex is numbered^ according to the 5S rRNA gene. (B) The six-finger protein corresponds to amino acid residues 1-190 of X. laevis TFIIIA (42, 43). Zinc fingers are aligned to show their secondary structure. Beta^ sheet is indicated by open arrows and the alpha helix is indicated^ as an open box. The "TA" region of TFIIIA is required for transcription activation (56) and "NE" is required for nuclear export (4).

Figure 3.
Fig. 3. DNA major-groove contacts with each of the zinc fingers 1, 2, 3, and 5. (A-D) The zinc fingers are placed in similar orientations. The protein is shown as a ribbon with alpha helix, blue, and beta^ sheet, green. The DNA is light blue. The amino acid side chains that contact nucleotide bases are yellow, and hydrogen-bond contacts are shown as dotted lines. Oxygen atoms are red, and nitrogen, magenta. (E-H) The major groove of DNA is represented schematically in cylindrical projection. The noncoding strand is numbered as in the 5S rRNA gene. Nucleotide bases of the "canonical" quartet for contacts by zinc fingers in previously analyzed structures are shown shaded, as are two phosphates that frequently receive^ hydrogen bonds. Contacts between amino acids and DNA are drawn as arrows.

Figures were selected by an automated process.