Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14087.27 
• Atom Count: 964 
• Residue Count: 92 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

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
• Organism(s): Homo sapiens
• Mutation(s): 2 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.228 
• R-Value Work: 0.192 

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 
• DOI: 10.1038/35002634


• 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.

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Related Citations: 

• 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
• 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
• 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
• 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
• 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




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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	Homo sapiens	Mutation(s): 2  Gene Names: RFX1
Find proteins for P22670 (Homo sapiens) Go to Gene View: RFX1 Go to UniProtKB:  P22670

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')	D	16	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	P	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
PEG	P	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BRU	D	DNA LINKING	C9 H12 Br N2 O8 P		DU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.228 
• R-Value Work: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 72.843	α = 90.00
b = 42.752	β = 109.21
c = 52.277	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2000-03-06
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance