Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.09 kDa 
• Atom Count: 1088 
• Modelled Residue Count: 92 
• Deposited 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

• PDB DOI: 10.2210/pdb1DP7/pdb

• 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.

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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 

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
• Primary Citation of Related Structures:  
  1DP7


• 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: 

• 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

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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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS II TRANSCRIPTION FACTOR HRFX1	B [auth P]	76	N/A	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P22670 (Homo sapiens) Explore P22670  Go to UniProtKB:  P22670
PHAROS:  P22670

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth P]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth P], D [auth P]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.228 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.843	α = 90
b = 42.752	β = 109.21
c = 52.277	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2021-11-03
  Changes: Database references