7VUP: NF-kB p52 homodimer

Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment. Determined by X-ray diffraction at 3.4 Å resolution. Released 24 Nov 2021.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,359
Mol. weight: 98.5 kDa
Released: 24 Nov 2021

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

Secondary structure: helices and β-sheets

7VUP contains 20 α-helices and 60 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: 11 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	39-44	6	1
α-helix	45	1
β-strand	46	1	2
α-helix	47	1
β-strand	51	1	3
α-helix	52-53	2
β-strand	54-55	2	4
β-strand	67	1	2
β-strand	79-83	5	1
β-strand	89-96	8	5
α-helix	103	1
β-strand	104	1	5
α-helix	105	1
β-strand	108-110	3	4
β-strand	114	1	5
β-strand	120-124	5	5
β-strand	130-132	3	1
β-strand	137-140	4	4
α-helix	141-142	2
α-helix	146-157	12
α-helix	168-182	15
β-strand	189-190	2	6
β-strand	191-198	8	5
β-strand	207-208	2	5
β-strand	212-213	2	5
α-helix	214-216	3
β-strand	217-218	2	6
β-strand	219	1	3
β-strand	230-233	4	7
β-strand	237-239	3	8
β-strand	245-250	6	7
β-strand	259-263	5	8
β-strand	271-273	3	8
β-strand	275	1	7
α-helix	278-280	3
β-strand	281-282	2	7
β-strand	286-290	5	7
α-helix	291-294	4
β-strand	303-310	8	8
β-strand	317	1	8
β-strand	321-326	6	8

Chain B: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	39-44	6	9
α-helix	45	1
β-strand	46	1	10
α-helix	47	1
β-strand	51	1	11
α-helix	52-53	2
β-strand	54-55	2	12
β-strand	67	1	10
β-strand	79-83	5	9
β-strand	89-96	8	13
β-strand	104	1	13
β-strand	108-110	3	12
β-strand	114	1	13
β-strand	120-124	5	13
β-strand	130-132	3	9
β-strand	137-140	4	12
α-helix	141-142	2
α-helix	146-157	12
α-helix	168-182	15
β-strand	189-190	2	14
β-strand	191-198	8	13
β-strand	207-208	2	13
β-strand	212-213	2	13
α-helix	214-216	3
β-strand	217-218	2	14
β-strand	219	1	11
β-strand	230-233	4	15
β-strand	237-239	3	16
β-strand	245-250	6	15
β-strand	258-263	6	16
β-strand	271-273	3	16
β-strand	275	1	15
α-helix	278-280	3
β-strand	281-282	2	15
β-strand	286-290	5	15
α-helix	291-294	4
β-strand	303-311	9	16
β-strand	317	1	16
β-strand	321-326	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear factor NF-kappa-B p52 subunit	A, B	protein	398	Homo sapiens	Q00653 (AlphaFold model)
DNA (5'-d(cpapapgpgpgpgpapcptpcpcpcpcpcptp*t)-3')	C	DNA	18	Homo sapiens
DNA (5'-d(apapgpgpgpgpgpapgptpcpcpcpcptptp*g)-3')	D	DNA	18	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7VUP_1 Nuclear factor NF-kappa-B p52 subunit (chains A, B)
MESCYNPGLDGIIEYDDFKLNSSIVEPKEPAPETADGPYLVIVEQPKQRGFRFRYGCEGP
SHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGIC
AVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKE
LKKVMDLSIVRLRFSAFLRASDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSV
RGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIE
RPVTVFLQLKRKRGGDVSDSKQFTYYPLVEDKEEVQRKRRKALPTFSQPFGGGSHMGGGS
GGAAGGYGGAGGGGSLGFFPSSLAYSPYQSGAGPMGCY

Sequence of entity 2 (C), FASTA

>7VUP_2 DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3') (chains C)
CAAGGGGACTCCCCCTTC

Sequence of entity 3 (D), FASTA

>7VUP_3 DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3') (chains D)
GAAGGGGGAGTCCCCTTG

Primary citation

Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. Pan, W., Meshcheryakov, V.A., Li, T. et al. Elife (2023) 12. DOI 10.7554/eLife.86258 · PubMed

Other PDB entries of the same protein (UniProt Q00653 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1A3Q 2.1 Å, Human nf-kappa-B P52 bound to DNA
8G8S 2.1 Å, bipartite p52 NLS in complex with Importin alpha 2
8G8Q 2.6 Å, Monopartite p52 NLS in complex with Importin alpha 2
5ZMC 2.99 Å, Structural Basis for Reactivation of -146C>T Mutant TERT Promoter by cooperative binding…
7CLI 3.0 Å, Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment
7W7L 3.0 Å, Structure of NF-kB p52 homodimer bound to 13-mer A/T-centric P-Selectin kB DNA fragment
3DO7 3.05 Å, X-ray structure of a NF-kB p52/RelB/DNA complex
7VUQ 3.1 Å, Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment
4OT9 3.35 Å, crystal structure of the C-terminal domain of p100/NF-kB2
2D96 Solution structure of the Death domain of Nuclear factor NF-kappa-B p100

Browse structure collections

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