PDBsum entry 4xrs

Transcription

PDB id: 4xrs

Contents

Protein chains

56 a.a.

58 a.a.

56 a.a.

DNA/RNA

PDB id:

4xrs

Name:

Transcription

Title:

Heterodimeric complex of transcription factors meis1 and dlx3 on specific DNA

Structure:

DNA (5'-d(p Cp Ap Ap Tp Tp Ap Tp Cp Cp Tp Gp Tp Cp Ap A)- 3'). Chain: m. Engineered: yes. DNA (5'- d(p Ap Cp Ap Ap Tp Tp Ap Tp Cp Cp Tp Gp Tp Cp Ap Ap C)-3'). Chain: d. Engineered: yes. DNA (5'-

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Homo sapiens. Human. Organism_taxid: 9606. Gene: meis1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

3.50Å R-factor: 0.343 R-free: 0.359

Authors:

A.Jorma,Y.Yin,K.R.Nitta,K.Dave,M.Enge,T.Kivioja,A.Popov,E.Morgunova, J.Taipale

Key ref:

A.Jolma et al. (2015). DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature, 527, 384-388. PubMed id: 26550823 DOI: 10.1038/nature15518

Date:

21-Jan-15 Release date: 04-Nov-15

Protein chain

O00470  (MEIS1_HUMAN) -  Homeobox protein Meis1 from Homo sapiens

Seq: 390 a.a.

Struc: 56 a.a.

Protein chain

O00470  (MEIS1_HUMAN) -  Homeobox protein Meis1 from Homo sapiens

Seq: 390 a.a.

Struc: 58 a.a.

Protein chains

O60479  (DLX3_HUMAN) -  Homeobox protein DLX-3 from Homo sapiens

Seq: 287 a.a.

Struc: 56 a.a.

DNA/RNA chains

C-A-A-T-T-A-T-C-C-T-G-T-C-A-A 15 bases

A-C-A-A-T-T-A-T-C-C-T-G-T-C-A-A-C 17 bases

G-T-T-G-A-C-A-G-G-A-T-A-A-T-T-G-T-T 18 bases

T-T-G-A-C-A-G-G-A-T-A-A-T-T-G-T 16 bases

DOI no: 10.1038/nature15518

Nature 527:384-388 (2015)

PubMed id: 26550823

DNA-dependent formation of transcription factor pairs alters their binding specificity.

A.Jolma, Y.Yin, K.R.Nitta, K.Dave, A.Popov, M.Taipale, M.Enge, T.Kivioja, E.Morgunova, J.Taipale.

ABSTRACT

Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.