1DP7

COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE

DOI: 10.2210/pdb1DP7/pdb
NDB: PD0111

Classification: TRANSCRIPTION/DNA
Mutation(s): Yes

Deposited: 1999-12-23 Released: 2000-03-06
Deposition Author(s): Gajiwala, K.S., Chen, H., Cornille, F., Roques, B.P., Reith, W., Mach, B., Burley, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.228
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

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

(2000) Nature 403: 916-921

PubMed: 10706293 Search on PubMed
DOI: 10.1038/35002634
Structures With Same Primary Citation

PubMed 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.

Related Citations:

Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5
Clark, K.L., Halay, E.D., Lai, E., Burley, S.K.
(1993) Nature 364: 412

Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
Ramakrishnan, V., Finch, J., Graziano, V., Sweet, R.
(1993) Nature 362: 219

A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity
Emery, P., Strubin, M., Hofmann, K., Bucher, P., Mach, B., Reith, W.
(1996) Mol Cell Biol 16: 4486

RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins
Reith, W., Ucla, C., Barras, E., Gaud, A., Durand, B., Herrero-Sanchez, C., Kobr, M., Mach, B.
(1994) Mol Cell Biol 14: 1230

DNA binding properties of a chemically synthesized DNA binding domain of hRFX1
Cornille, F., Emery, P., Schuler, W., Lenoir, C., Mach, B., Roques, B.P., Reith, W.
(1998) Nucleic Acids Res 26: 2143

Organizational Affiliation:

Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
MHC CLASS II TRANSCRIPTION FACTOR HRFX1	P	76	N/A	Mutation(s): 2
Find proteins for P22670 (Homo sapiens) Go to UniProtKB: P22670
NIH Common Fund Data Resources
PHAROS P22670 GTEx ENSG00000132005
Protein Feature View Full Protein Feature View for P22670

Find similar nucleic acids by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(CPGP(BRU)PTPAPCPCPAP(BRU)PGPGPTPAPAPCPG)-3')	D	16	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download CCD File	P	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download CCD File	P	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction