7O56: Interferon regulatory factor 4

X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element solved by Phosphorus and Sulphur SAD methods. Determined by X-ray diffraction at 2.6 Å resolution. Released 12 May 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 3,666
Mol. weight: 61.8 kDa
Released: 12 May 2021

Explore 7O56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O56 contains 11 α-helices and 15 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-33	10
β-strand	41-42	2	1
β-strand	49-53	5	1
α-helix	64-77	14
α-helix	90-103	14
β-strand	107-109	3	1
β-strand	115	1	1
β-strand	122-127	6	1
α-helix	128-131	4

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-33	10
β-strand	41-42	2	2
β-strand	49-53	5	2
α-helix	64-77	14
α-helix	90-103	14
β-strand	107-109	3	2
β-strand	115	1	2
β-strand	122-127	6	2
α-helix	128-129	2

Chain C: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-33	10
β-strand	42	1	3
β-strand	49-53	5	3
α-helix	64-77	14
α-helix	90-103	14
β-strand	107-109	3	3
β-strand	115	1	3
β-strand	122-127	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon regulatory factor 4	A, B, C	protein	141	Homo sapiens	Q15306 (AlphaFold model)
DNA (5'-d(papaptpapapapapgpapapapcpcpgpapapapgptpap*a)-3')	D	DNA	21	synthetic construct
DNA (5'-d(ptptptpapcptptptpcpgpgptptptpcptptptptpap*t)-3')	E	DNA	21	synthetic construct

Sequence of entity 1 (A, B, C), FASTA

>7O56_1 Interferon regulatory factor 4 (chains A, B, C)
MGSHHHHHHSAALEVLFQGPGGNGKLRQWLIDQIDSGKYPGLVWENEEKSIFRIPWKHAG
KQDYNREEDAALFKAWALFKGKFREGIDKPDPPTWKTRLRCALNKSNDFEELVERSQLDI
SDPYKVYRIVPEGAKKGAKQL

Sequence of entity 2 (D), FASTA

>7O56_2 DNA (5'-D(P*AP*AP*TP*AP*AP*AP*AP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*A)-3') (chains D)
AATAAAAGAAACCGAAAGTAA

Sequence of entity 3 (E), FASTA

>7O56_3 DNA (5'-D(P*TP*TP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*TP*TP*TP*TP*AP*T)-3') (chains E)
TTTACTTTCGGTTTCTTTTAT

Primary citation

Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4. Agnarelli, A., El Omari, K., Duman, R. et al. Acta Crystallogr F Struct Biol Commun (2021) 77:202-207. DOI 10.1107/S2053230X21006506 · PubMed

Other PDB entries of the same protein (UniProt Q15306 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TD4 1.71 Å, IRF4 DNA-binding domain surface entropy mutant apo structure
9VEH 2.0 Å, The MIDN Catch-IRF4 (A8M) fusion protein
9TOY 2.1 Å, Investigating the binding mechanism of Interferon Regulatory Factor 4 to DNA in the…
9VE3 2.1 Å, The MIDN Catch-IRF4 (V2L) fusion protein
9VE7 2.15 Å, The MIDN Catch-IRF4 (A8V) fusion protein
7OOT 2.25 Å, X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an…
7OGS 2.37 Å, X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an…
7RH2 2.47 Å, IRF4 Transcription factor mutant -K59R
9CUG 2.49 Å, X-ray Structure of human Interferon Regulatory Factor 4 (IRF4) IAD Domain
9VE4 2.55 Å, The MIDN Catch-IRF4 fusion protein
9VE6 2.8 Å, The MIDN Catch-IRF4 (F6Y) fusion protein
9VE8 2.85 Å, The MIDN Catch-IRF4 (A8L) fusion protein

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