PDBsum entry: 1cit

Transcription/DNA

PDB id: 1cit

Contents

Protein chain

89 a.a. *

DNA/RNA

Metals

_ZN ×2

Waters ×38

* Residue conservation analysis

PDB id:

1cit

Name:

Transcription/DNA

Title:

DNA-binding mechanism of the monomeric orphan nuclear receptor ngfi-b

Structure:

DNA (5'- d( Cp Cp Gp Ap Ap Ap Ap Gp Gp Tp Cp Ap Tp Gp Cp G)-3'). Chain: b. Engineered: yes. DNA (5'- d( Cp Gp Cp Ap Tp Gp Ap Cp Cp Tp Tp Tp Tp Cp Gp G)-3'). Chain: c. Engineered: yes. Protein (orphan nuclear receptor ngfi-b).

Source:

Synthetic: yes. Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: brain. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.70Å R-factor: 0.219 R-free: 0.295

Authors:

G.Meinke,P.B.Sigler

Key ref:

G.Meinke and P.B.Sigler (1999). DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B. Nat Struct Biol, 6, 471-477. PubMed id: 10331876 DOI: 10.1038/8276

Date:

05-Apr-99 Release date: 03-May-99

Protein chain

P22829  (NR4A1_RAT) -  Nuclear receptor subfamily 4 group A member 1

Seq: 597 a.a.

Struc: 89 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: DNA binding (6 terms)

DOI no: 10.1038/8276

Nat Struct Biol 6:471-477 (1999)

PubMed id: 10331876

DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B.

G.Meinke, P.B.Sigler.

ABSTRACT

The 2.7 A X-ray crystal structure of the DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B), complexed to its high-affinity DNA target, represents the first structure analysis of a nuclear receptor DBD bound as a monomer to DNA. The structure of the core DBD and its interactions with the major groove of the DNA are similar to previously crystallographically solved DBD-DNA complexes in this superfamily; however, residues C-terminal to this core form a separate and unique substructure that interacts extensively and in a sequence-specific way with the minor groove of its DNA target, in particular with the characteristic 3 A-T base-pair identity element that extends 5' to the usual nuclear receptor half-site (AGGTCA).

Selected figure(s)

Figure 1.
Figure 1. Sequences of the macromolecular components. Top panel shows domain structure of NGFI-B. a, Amino acid sequence of rat NGFI-B used in crystallographic analyses. The sequence depicts the Zn-Cys coordination. The numbering is that of the full-length receptor. Residues in red, magenta, blue, green indicate the P-box, D-box, T-box and A-box, respectively. Solid lines box indicate -helical segments, dashed lines indicate disordered regions. b, The DNA sequence in the crystal. The canonical estrogen response element (ERE) half-site and the required 5'-flanking sequence AAA are shown in green and pink boxes, respectively. DNA is numbered with the origin at the junction of the half-site and the 5' extension; numbers in the bottom strand are 'primed'.

Figure 3.
Figure 3. a, Stereo diagram of CTE of NGFI-B interacting with minor groove of its DNA target (RIBBONS^39). Coloring as in Fig. 2. Functional groups in the minor groove are displayed as slightly larger spheres and colored red (oxygen) or cyan (nitrogen). Hydrogen bonds are indicated by dashed lines (HBPLUS^15). b, Stereo view of the sigma A^36-weighted (2|F[o]| - |F[c]|) electron density map (SETOR^41) contoured at 1.2 (lavender) and 4 (red), showing where Arg 311-Gly 312-Arg 313 motif interacts in the minor groove of the DNA. Atoms/bonds are colored by atom type: carbon, green; nitrogen, blue; oxygen, red; phosphate, magenta. Base pairs A[1]-T[1'] and G[2]-C[ 2'] are the first two base pairs of the canonical half-site. c, Summary of protein−DNA contacts for both major and minor grooves. The ERE half-site and the 5'-A[-3]A[-2]A[-1] are shown in green and pink, respectively. Backbone and side-chain interactions are indicated by dashed and solid lines, respectively. Hydrogen bonds are indicated as blue arrows, pointing from donor to acceptor (HBPLUS^42).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 471-477) copyright 1999.

Figures were selected by the author.