7RH2: IRF4 Transcription factor mutant -K59R

Name: PDB 7RH2: IRF4 Transcription factor mutant -K59R
Published: 2022-05-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

IRF4 Transcription factor mutant -K59R. Determined by X-ray diffraction at 2.47 Å resolution. Released 25 May 2022.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 8
Atoms: 5,209
Mol. weight: 75.83 kDa
Released: 25 May 2022

Explore 7RH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RH2 contains 20 α-helices and 20 β-strands across 4 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: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-34	11
β-strand	41-42	2	1
β-strand	49-53	5	1
α-helix	68-77	10
α-helix	87-88	2
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	1

Chain B: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-34	11
β-strand	41-42	2	2
β-strand	49-53	5	2
α-helix	55-56	2
α-helix	64-77	14
α-helix	87-88	2
α-helix	90-103	14
β-strand	107-109	3	2
β-strand	115	1	2
β-strand	122-127	6	2

Chain G: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-34	11
β-strand	41-42	2	3
β-strand	49-53	5	3
α-helix	55-56	2
α-helix	64-67	4
α-helix	69-77	9
α-helix	87-88	2
α-helix	90-103	14
β-strand	107-109	3	3
β-strand	115	1	3
β-strand	122-127	6	3

Chain H: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-34	11
β-strand	41-42	2	4
β-strand	49-53	5	4
α-helix	68-77	10
α-helix	87-88	2
α-helix	90-103	14
β-strand	107-109	3	4
β-strand	115	1	4
β-strand	122-127	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ICSAT transcription factor	A, B, G, H	protein	111	Homo sapiens	Q15306 (AlphaFold model)
DNA (5'-d(cpapapcptpgpapapapcpcpgpapgpapapapgp*c)-3')	C, D	DNA	19	Homo sapiens
DNA (5'-d(gpcptptptpcptpcpgpgptptptpcpapgptptp*g)-3')	E, F	DNA	19	Homo sapiens

Sequence of entity 1 (A, B, G, H), FASTA

>7RH2_1 ICSAT transcription factor (chains A, B, G, H)
GSNGKLRQWLIDQIDSGKYPGLVWENEEKSIFRIPWKHAGRQDYNREEDAALFKAWALFK
GKFREGIDKPDPPTWKTRLRCALNKSNDFEELVERSQLDISDPYKVYRIVP

Sequence of entity 2 (C, D), FASTA

>7RH2_2 DNA (5'-D(*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*AP*AP*AP*GP*C)-3') (chains C, D)
CAACTGAAACCGAGAAAGC

Sequence of entity 3 (E, F), FASTA

>7RH2_3 DNA (5'-D(*GP*CP*TP*TP*TP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3') (chains E, F)
GCTTTCTCGGTTTCAGTTG

Primary citation

The molecular basis for the development of adult T-cell leukemia/lymphoma in patients with an IRF4 K59R mutation. Sundararaj, S., Seneviratne, S., Williams, S.J. et al. Protein Sci (2022) 31:787-796. DOI 10.1002/pro.4260 · 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…
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
7O56 2.6 Å, X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an…
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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