3DO7: NF-kB p52/RelB/DNA complex

X-ray structure of a NF-kB p52/RelB/DNA complex. Determined by X-ray diffraction at 3.05 Å resolution. Released 21 Jul 2009.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 5,288
Mol. weight: 76.54 kDa
Released: 21 Jul 2009

Explore 3DO7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DO7 contains 10 α-helices and 63 β-strands across 2 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: 3 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	104-107	4	1
β-strand	111	1	2
β-strand	114-116	3	3
β-strand	119	1	4
β-strand	132	1	2
β-strand	144-148	5	1
β-strand	157	1	5
β-strand	160-163	4	6
β-strand	171	1	6
β-strand	175-178	4	4
β-strand	181	1	6
β-strand	185-186	2	6
β-strand	197-199	3	1
β-strand	203-206	4	4
α-helix	213-222	10
β-strand	243-244	2	3
β-strand	245-248	4	6
β-strand	251	1	5
β-strand	261	1	5
β-strand	265	1	6
β-strand	270-272	3	3
β-strand	283-286	4	7
β-strand	290-292	3	8
β-strand	297-299	3	9
β-strand	301-303	3	7
β-strand	312-314	3	10
β-strand	323	1	10
β-strand	325	1	9
α-helix	328-330	3
β-strand	331	1	11
α-helix	332-334	3
β-strand	336	1	7
β-strand	337	1	11
β-strand	339-341	3	9
β-strand	353-357	5	8
β-strand	358-360	3	10
β-strand	371-376	6	8

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	12
α-helix	45	1
β-strand	46	1	13
α-helix	47	1
β-strand	49	1	14
β-strand	54-55	2	15
α-helix	56-58	3
β-strand	67	1	13
β-strand	71	1	16
β-strand	74	1	16
β-strand	79-83	5	12
β-strand	89-97	9	14
β-strand	109-110	2	17
β-strand	118	1	17
β-strand	120-124	5	14
β-strand	130-132	3	12
β-strand	137-138	2	17
β-strand	139-140	2	15
α-helix	146-155	10
α-helix	156-160	5
α-helix	168-182	15
β-strand	189-197	9	14
β-strand	198-199	2	18
β-strand	205-207	3	18
β-strand	212-213	2	14
β-strand	217-218	2	14
β-strand	232-233	2	19
β-strand	245-249	5	19
β-strand	259	1	20
β-strand	262-263	2	21
α-helix	278-280	3
β-strand	281	1	19
β-strand	286-290	5	19
β-strand	305-307	3	21
β-strand	310	1	20
β-strand	321-323	3	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(dcpdgpdgpdgpdapdapdtpdtpdcpdcp*dc)-3'	C, D, E	DNA	11
Avian reticuloendotheliosis viral (V-rel) oncogene related B	A	protein	296	Mus musculus	Q04863 (AlphaFold model)
Nuclear factor NF-kappa-B p100 subunit	B	protein	293	Homo sapiens	Q00653 (AlphaFold model)

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

>3DO7_1 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3' (chains C, D, E)
CGGGAATTCCC

Sequence of entity 2 (A), FASTA

>3DO7_2 Avian reticuloendotheliosis viral (V-rel) oncogene related B (chains A)
SCTLGRLVSPGPCPRPYLVITEQPKQRGMRFRYECEGRSAGSILGESSTEASKTQPAIEL
RDCGGLREVEVTACLVWKDWPHRVHPHSLVGKDCTDGVCRVRLRPHVSPRHSFNNLGIQC
VRKKEIEAAIERKIQLGIDPYNAGSLKNHQEVDMNVVRICFQASYRDQQGHLHRMDPILS
EPVYDKKSTNTSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTASWEGRADFS
QADVHRQIAIVFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLPRDHDSY

Sequence of entity 3 (B), FASTA

>3DO7_3 Nuclear factor NF-kappa-B p100 subunit (chains B)
GPYLVIVEQPKQRGFRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLV
THSDPPRAHAHSLVGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQR
QRLRSRPQGLTEAEQRELEQEAKELKKVMDLSIVRLRFSAFLRDSDGSFSLPLKPVISQP
IHDSKSPGASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDF
SPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPLV

Primary citation

NF-kapppaB p52:RelB heterodimer uses different binding modes to recognize different kappaB DNA. Fusco, A., Huang, D.B., Miller, D. et al. To be published.

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
3JV4 3.15 Å, Crystal structure of the dimerization domains p50 and RelB

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