PDBsum entry 5zjs

Transcription/DNA

PDB id: 5zjs

Contents

Protein chains

58 a.a.

72 a.a.

DNA/RNA

Waters ×3

PDB id:

5zjs

Name:

Transcription/DNA

Title:

Structure of abdb/exd complex bound to a 'blue14' DNA sequence

Structure:

Homeobox protein abdominal-b. Chain: a. Synonym: infraabdominal 7,iab-7,p3,ph189. Engineered: yes. Homeobox protein extradenticle. Chain: b. Synonym: dpbx. Engineered: yes. DNA (5'-d( Gp Tp Cp Ap Tp Tp Ap Ap Tp Cp Ap Tp Gp C)-3').

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: abd-b, cg10291. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: exd, cg8933. Synthetic: yes. Organism_taxid: 7227

Resolution:

2.90Å R-factor: 0.255 R-free: 0.281

Authors:

N.Baburajendran,T.Zeiske,A.Kaczynska,R.Mann,B.Honig,L.Shapiro, A.G.Palmer

Key ref:

T.Zeiske et al. (2018). Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Cell Rep, 24, 2221-2230. PubMed id: 30157419 DOI: 10.1016/j.celrep.2018.07.100

Date:

22-Mar-18 Release date: 29-Aug-18

Protein chain

P09087  (ABDB_DROME) -  Homeobox protein abdominal-B from Drosophila melanogaster

Seq: 493 a.a.

Struc: 58 a.a.*

Protein chain

P40427  (EXD_DROME) -  Homeobox protein extradenticle from Drosophila melanogaster

Seq: 376 a.a.

Struc: 72 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-T-C-A-T-T-A-A-T-C-A-T-G-C 14 bases

G-C-A-T-G-A-T-T-A-A-T-G-A-C 14 bases

DOI no: 10.1016/j.celrep.2018.07.100

Cell Rep 24:2221-2230 (2018)

PubMed id: 30157419

Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

T.Zeiske, N.Baburajendran, A.Kaczynska, J.Brasch, A.G.Palmer, L.Shapiro, B.Honig, R.S.Mann.

ABSTRACT

Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to ∼20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.