PDBsum entry: 1a3q

Transcription/DNA

PDB-id: 1a3q

Biological unit = asymmetric unit, as shown
(as defined in PDB file)

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References

PROCHECK

Protein chains

285 a.a. *

DNA/RNA

Waters ×785

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1a3q

Name:

Transcription/DNA

Title:

Human nf-kappa-b p52 bound to DNA

Structure:

DNA (5'-d( Gp Gp Gp Gp Ap Ap Tp Cp Cp Cp C)-3'). Chain: c. Engineered: yes. DNA (5'-d( Gp Gp Gp Gp Ap Tp Tp Cp Cp Cp C)-3'). Chain: d. Engineered: yes. Protein (nuclear factor kappa-b p52). Chain: a, b. Synonym: nuclear factor kappa-b p52.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Undecamer (from PDB file)

UniProt:

Chains A, B: Q00653 (NFKB2_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

900 a.a.

Struc:

285 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.10Å

R-factor:

0.219

R-free:

0.320

Authors:

P.Cramer,C.J.Larson,G.L.Verdine,C.W.Muller

Key ref:

P.Cramer et al. (1997). Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.. EMBO J, 16, 7078-7090. [PubMed id: 9384586] [DOI: 10.1093/emboj/16.23.7078]

Date:

23-Jan-98

Release date:

11-Jun-98

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Clefts

Surface

Key reference

DOI no: 10.1093/emboj/16.23.7078

EMBO J 16:7078-7090 (1997)

PubMed id: 9384586

Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.

P.Cramer, C.J.Larson, G.L.Verdine, C.W.Müller.

ABSTRACT

The crystal structure of human NF-kappaB p52 in its specific complex with the natural kappaB DNA binding site MHC H-2 has been solved at 2.1 A resolution. Whereas the overall structure resembles that of the NF-kappaB p50-DNA complex, pronounced differences are observed within the 'insert region'. This sequence segment differs in length between different Rel proteins. Compared with NF-kappaB p50, the compact alpha-helical insert region element is rotated away from the core of the N-terminal domain, opening up a mainly polar cleft. The insert region presents potential interaction surfaces to other proteins. The high resolution of the structure reveals many water molecules which mediate interactions in the protein-DNA interface. Additional complexity in Rel protein-DNA interaction comes from an extended interfacial water cavity that connects residues at the edge of the dimer interface to the central DNA bases. The observed water network might acount for differences in binding specificity between NF-kappaB p52 and NF-kappaB p50 homodimers.

Selected figure(s)

Figure 2.
Figure 2 (A) Overall view of the NF- B p52 homodimer -DNA complex structure along the DNA helical axis with the approximate dyad vertical. The DNA duplex is in blue. Color coding for the protein is as in Figure 1A. Secondary structure elements are labeled. DNA-contacting loops are labeled for monomer I. The disordered loop HI is drawn as a dashed line. (B) Stereo view of rearrangement of the N-terminal domains upon DNA binding, based on superposition of the C-terminal domains of both crystallographically independent monomers. The protein chains are drawn as C -traces (monomer I and II as thick and thin lines, respectively). The view is approximately perpendicular to that in (A). The DNA is shown in its relative position to monomer I. The -helices A and B and the N- and C-termini are labeled. (C) Structural comparison of the N-terminal domains of NF- B p52 (yellow) and NF- B p50 (green) based on superposition of C atoms of the N-terminal domain core. The view is similar to that in (B). The protein structures are represented as backbone traces. The helices within the insert region are emphasized.

Figure 5.
Figure 5 DNA recognition by the NF- B p52 homodimer. (A) Schematic diagram of polar interactions between protein and DNA. Contacts to DNA bases (yellow boxes), to the DNA backbone (red boxes) and water-mediated contacts (green boxes) in both half sites are shown. Water molecules are depicted as green spheres. (B) Stereo view of DNA base-specific recognition in the first half site. Protein residues and DNA bases are drawn with filled and open bonds, respectively. Water molecules are drawn as open spheres. DNA backbone atoms have been omitted for clarity. Polar interactions are indicated as broken lines.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 7078-7090) copyright 1997.

Figures were selected by the author.