PDBsum entry 1dp7

Transcription/DNA

PDB id: 1dp7

Contents

Protein chain

76 a.a. *

DNA/RNA

Ligands

EDO ×2

PEG

Waters ×124

* Residue conservation analysis

PDB id:

1dp7

Name:

Transcription/DNA

Title:

Cocrystal structure of rfx-dbd in complex with its cognate x-box binding site

Structure:

DNA (5'-d( Cp Gp (Bru)p Tp Ap Cp Cp Ap (Bru) p Gp Gp Tp Ap Ap Cp G)-3'). Chain: d. Fragment: x-box. Engineered: yes. Mhc class ii transcription factor hrfx1. Chain: p. Fragment: DNA binding domain. Synonym: regulatory factor x.

Source:

Synthetic: yes. Other_details: sequence taken from human mhc class ii transcription factor

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.50Å R-factor: 0.192 R-free: 0.228

Authors:

K.S.Gajiwala,H.Chen,F.Cornille,B.P.Roques,W.Reith,B.Mach,S.K.Burley

Key ref:

K.S.Gajiwala et al. (2000). Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature, 403, 916-921. PubMed id: 10706293 DOI: 10.1038/35002634

Date:

23-Dec-99 Release date: 06-Mar-00

Protein chain

P22670  (RFX1_HUMAN) -  MHC class II regulatory factor RFX1 from Homo sapiens

Seq: 979 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chain

C-G-BRU-T-A-C-C-A-BRU-G-G-T-A-A-C-G 16 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/35002634

Nature 403:916-921 (2000)

PubMed id: 10706293

Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding.

K.S.Gajiwala, H.Chen, F.Cornille, B.P.Roques, W.Reith, B.Mach, S.K.Burley.

ABSTRACT

Regulatory factor X (RFX) proteins are transcriptional activators that recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD). DNA-binding defects in the protein RFX5 cause bare lymphocyte syndrome or major histocompatibility antigen class II deficiency. RFX1, -2 and -3 regulate expression of other medically important gene products (for example, interleukin-5 receptor alpha chain, IL-5R alpha). Fusions of the ligand-binding domain of the oestrogen receptor with the DBD of RFX4 occur in some human breast tumours. Here we present a 1.5 A-resolution structure of two copies of the DBD of human RFX1 (hRFX1) binding cooperatively to a symmetrical X-box. hRFX1 is an unusual member of the winged-helix subfamily of helix-turn-helix proteins because it uses a beta-hairpin (or wing) to recognize DNA instead of the recognition helix typical of helix-turn-helix proteins. A new model for interactions between linker histones and DNA is proposed.

Selected figure(s)

Figure 2.
Figure 2: RFX1 and HNF-3 bold gamma-DBDs. a, hRFX1 DBD with labelled N and C termini and secondary structural elements (HTH recognition helix H3, red). b, Superposition of hRFX1 and HNF-3 DBDs (r.m.s. deviation for -carbon atoms, 3.5 Å), shown in the same orientation as a. c, Stereo diagram of the hRFX1-DNA 2:1 complex, viewed along the 2-fold crystallographic symmetry axis relating each half of the asymmetric unit. Inset, crystallization oligonucleotide, with blue characters denoting X-box half-sites, labelled A and B. d, Stereo diagram of HNF-3 bound to its cognate DNA^6.

Figure 3.
Figure 3: Protein-DNA interactions. a, Representative 1.5 Å resolution electron-density map contoured at 2 , showing Arg 82 bound to G11 in the major groove of the B half-site. The crystallization oligonucleotide is inset, with bold denoting each half-site, and an asterisk identifying the depicted nucleotide(s). b, Arg 62 bound to G15' in the major groove of the B halfsite. c, Lys 45 from H3 (red) interacts with the minor groove face of the A half-site. Red spheres denote water molecules. d, Direct and water-mediated protein-DNA contacts made by W1 with the phospho-deoxyribose backbones, flanking the major groove of the B half-site.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 403, 916-921) copyright 2000.

Figures were selected by an automated process.