3JV6: Dimerization domains p52 and RelB

Crystal structure of the dimerization domains p52 and RelB. Determined by X-ray diffraction at 2.78 Å resolution. Released 24 Nov 2010.

Method: X-ray diffraction
Resolution: 2.78 Å
Organism: Mus musculus
Chains: 6
Atoms: 5,191
Mol. weight: 72.38 kDa
Released: 24 Nov 2010

Explore 3JV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JV6 contains 17 α-helices and 68 β-strands across 6 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.

Chains A and E: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	283-286	4	1
β-strand	290-292	3	2
β-strand	298-303	6	1
β-strand	312-316	5	2
β-strand	321-323	3	2
β-strand	325	1	1
α-helix	328-330	3
α-helix	332-334	3
β-strand	336-340	5	1
α-helix	341-344	4
β-strand	353-360	8	2
β-strand	367	1	2
β-strand	371-376	6	2

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	226-227	2
β-strand	228	1	3
β-strand	230-233	4	4
β-strand	237-239	3	5
β-strand	245-250	6	4
β-strand	258-263	6	5
β-strand	271-273	3	5
β-strand	275	1	4
α-helix	278-280	3
β-strand	281-282	2	4
β-strand	286-290	5	4
α-helix	291-294	4
β-strand	303-311	9	5
β-strand	317	1	5
β-strand	318	1	3
β-strand	321-326	6	5

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	283-286	4	6
β-strand	290-292	3	7
β-strand	298-303	6	6
β-strand	312-316	5	7
β-strand	321-323	3	7
β-strand	325	1	6
α-helix	328-330	3
β-strand	331	1	6
α-helix	332-334	3
β-strand	336-340	5	6
α-helix	341-344	4
β-strand	353-360	8	7
β-strand	367	1	7
β-strand	371-376	6	7

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	230-233	4	8
β-strand	237-239	3	9
β-strand	245-250	6	8
β-strand	258-263	6	9
β-strand	271-273	3	9
β-strand	275	1	8
β-strand	281-282	2	8
β-strand	286-290	5	8
α-helix	291-294	4
β-strand	303-311	9	9
β-strand	317	1	9
β-strand	321-326	6	9

Chain F: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	226-227	2
β-strand	228	1	12
β-strand	230-233	4	13
β-strand	237-239	3	14
β-strand	245-250	6	13
β-strand	258-263	6	14
β-strand	271-273	3	14
β-strand	275	1	13
α-helix	278-280	3
β-strand	281-282	2	13
β-strand	286-290	5	13
α-helix	291-294	4
β-strand	303-311	9	14
β-strand	317	1	14
β-strand	318	1	12
β-strand	321-326	6	14
α-helix	327-328	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor RelB	A, C, E	protein	101	Mus musculus	Q04863 (AlphaFold model)
Nuclear factor NF-kappa-B p100 subunit	B, D, F	protein	107	Mus musculus	Q9WTK5 (AlphaFold model)

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

>3JV6_1 Transcription factor RelB (chains A, C, E)
TSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTASWEGRADFSQADVHRQIAI
VFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLPR

Sequence of entity 2 (B, D, F), FASTA

>3JV6_2 Nuclear factor NF-kappa-B p100 subunit (chains B, D, F)
ASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQ
YAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPVVED

Primary citation

A structural basis for selective dimerization by NF-kappa B RelB. Vu, D., Huang, D.B., Vemu, A. et al. J Mol Biol (2013) 425:1934-1945. DOI 10.1016/j.jmb.2013.02.020 · PubMed

Other PDB entries of the same protein (UniProt Q04863 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ZK9 2.18 Å, NF-kB RelB forms an intertwined homodimer
1ZKA 2.2 Å, NF-kB RelB forms an intertwined homodimer, Y300S mutant
4JHB 2.44 Å, Crystal structure of RelB double mutants: Y300F/I335F
3JUZ 2.51 Å, Crystal structure of a mutant of RelB dimerization domain(M5)
3JSS 2.6 Å, Crystal structure of a mutant RelB dimerization domain
3JV0 2.65 Å, Crystal structure of a mutant of RelB dimerization domain(M6)
4JGM 3.0 Å, Crystal structure of RelB double mutants: Y300F/I335V
2V2T 3.05 Å, X-ray structure of a NF-kB p50-RelB-DNA complex
3DO7 3.05 Å, X-ray structure of a NF-kB p52/RelB/DNA complex
3JV4 3.15 Å, Crystal structure of the dimerization domains p50 and RelB

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