3JV4: Dimerization domains p50 and RelB

Crystal structure of the dimerization domains p50 and RelB. Determined by X-ray diffraction at 3.15 Å resolution. Released 24 Nov 2010.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Mus musculus
Chains: 6
Atoms: 5,185
Mol. weight: 74.38 kDa
Released: 24 Nov 2010

Explore 3JV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JV4 contains 19 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	283-286	4	1
β-strand	290-292	3	2
β-strand	298-299	2	3
β-strand	301-303	3	1
β-strand	314-316	3	2
β-strand	321-323	3	2
α-helix	324	1
β-strand	325	1	3
α-helix	328-330	3
β-strand	331-332	2	1
β-strand	336-337	2	1
β-strand	339-340	2	3
α-helix	341-344	4
β-strand	353-358	6	2
β-strand	371-376	6	2

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	4
β-strand	257-259	3	5
β-strand	265-270	6	4
β-strand	278-284	7	5
β-strand	292-295	4	5
β-strand	297	1	4
α-helix	304-306	3
β-strand	308-312	5	4
β-strand	325-333	9	5
β-strand	339	1	5
α-helix	340-342	3
β-strand	343-348	6	5

Chain C: 3 helices, 10 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	314-316	3	7
β-strand	321-323	3	7
α-helix	324	1
β-strand	325	1	6
α-helix	328-330	3
β-strand	331-332	2	6
β-strand	336-340	5	6
α-helix	341-344	4
β-strand	353-358	6	7
β-strand	371-376	6	7

Chain D: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	248	1	8
β-strand	250-253	4	9
β-strand	257-259	3	10
β-strand	265-270	6	9
β-strand	274	1	11
β-strand	277	1	11
β-strand	279-285	7	10
β-strand	291-295	5	10
β-strand	297	1	9
α-helix	300-302	3
β-strand	303	1	9
α-helix	304-306	3
β-strand	308-312	5	9
α-helix	313-316	4
β-strand	325-332	8	10
β-strand	340	1	8
α-helix	341-342	2
β-strand	343-348	6	10
α-helix	349-351	3

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	15
β-strand	257-259	3	16
β-strand	265-270	6	15
β-strand	278-284	7	16
β-strand	292-295	4	16
β-strand	297	1	15
α-helix	300-302	3
α-helix	304-306	3
β-strand	308-312	5	15
β-strand	325-333	9	16
β-strand	339	1	16
α-helix	340-342	3
β-strand	343-348	6	16

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 p105 subunit	B, D, F	protein	115	Mus musculus	P25799 (AlphaFold model)

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

>3JV4_1 Transcription factor RelB (chains A, C, E)
TSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTASWEGRADFSQADVHRQIAI
VFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLPR

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

>3JV4_2 Nuclear factor NF-kappa-B p105 subunit (chains B, D, F)
ASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVH
RQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQR

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)
3JV6 2.78 Å, Crystal structure of the dimerization domains p52 and RelB
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

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