9BDU: NF-kappaB RelA homo-dimer

NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA. Determined by X-ray diffraction at 2.03 Å resolution. Released 24 Apr 2024.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Mus musculus, synthetic construct
Chains: 4
Atoms: 5,577
Mol. weight: 77.68 kDa
Released: 24 Apr 2024

Explore 9BDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BDU contains 33 α-helices and 54 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: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	1
α-helix	26	1
β-strand	27	1	2
α-helix	28	1
β-strand	32	1	3
α-helix	33-34	2
β-strand	35	1	4
α-helix	46-47	2
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	71-77	7	5
α-helix	84	1
β-strand	85	1	5
α-helix	86	1
β-strand	89-91	3	4
β-strand	95-96	2	5
β-strand	99-103	5	5
α-helix	104-105	2
β-strand	110-112	3	1
β-strand	117-119	3	4
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
α-helix	147-149	3
β-strand	156-166	11	5
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-184	7	5
β-strand	185	1	3
α-helix	193-194	2
β-strand	196-199	4	6
β-strand	203-205	3	7
β-strand	211-216	6	6
β-strand	225-230	6	7
β-strand	233-236	4	7
β-strand	238	1	6
α-helix	241-243	3
β-strand	244-245	2	6
β-strand	249-253	5	6
α-helix	254-257	4
β-strand	266-274	9	7
β-strand	279-280	2	7
β-strand	284-289	6	7

Chain B: 18 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	8
α-helix	26	1
β-strand	27	1	9
α-helix	28	1
α-helix	32-34	3
β-strand	35	1	10
α-helix	37-39	3
α-helix	46-47	2
β-strand	48	1	9
β-strand	60-64	5	8
β-strand	71-77	7	11
α-helix	84	1
β-strand	85	1	11
α-helix	86	1
β-strand	89-91	3	10
β-strand	95-96	2	11
β-strand	99-103	5	11
α-helix	104-105	2
β-strand	110-112	3	8
β-strand	117-119	3	10
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
α-helix	145-147	3
β-strand	156-166	11	11
β-strand	172-174	3	11
α-helix	175-177	3
β-strand	178-184	7	11
α-helix	193-194	2
β-strand	196-199	4	12
β-strand	203-205	3	13
β-strand	211-216	6	12
β-strand	225-230	6	13
β-strand	233-236	4	13
β-strand	238	1	12
α-helix	241-243	3
β-strand	244	1	12
β-strand	249-253	5	12
α-helix	254-257	4
β-strand	266-274	9	13
β-strand	279-280	2	13
α-helix	281-283	3
β-strand	284-289	6	13
α-helix	290-291	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor p65	A, B	protein	287	Mus musculus	Q04207 (AlphaFold model)
DNA (5'-d(papcptpgpgpgpapapaptptpcpcpapgptpgpap*t)-3')	C	DNA	19	synthetic construct
DNA (5'-d(paptpcpapcptpgpgpapaptptptpcpcpcpapgp*t)-3')	D	DNA	19	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9BDU_1 Transcription factor p65 (chains A, B)
MPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLV
TKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTN
NNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKIC
RVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPY
ADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKR

Sequence of entity 2 (C), FASTA

>9BDU_2 DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3') (chains C)
ACTGGGAAATTCCAGTGAT

Sequence of entity 3 (D), FASTA

>9BDU_3 DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*GP*T)-3') (chains D)
ATCACTGGAATTTCCCAGT

Primary citation

Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA. Li, T., Shahabi, S., Biswas, T. et al. Proc Natl Acad Sci U S A (2024) 121:e2405555121-e2405555121. DOI 10.1073/pnas.2405555121 · PubMed

Other PDB entries of the same protein (UniProt Q04207 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MY7 1.49 Å, NF-kappaB p65 subunit dimerization domain homodimer N202R mutation
1MY5 1.8 Å, NF-kappaB p65 subunit dimerization domain homodimer
9BDW 1.87 Å, NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA
9BDV 1.9 Å, NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA
1BFT 2.0 Å, Structure of nf-kb P65 homodimer bound to a kb site
9E6W 2.04 Å, NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene
1OY3 2.05 Å, Crystal structure of an ikbbeta/nf-kb P65 homodimer complex
6GGR 2.1 Å, Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65
1IKN 2.3 Å, Ikappabalpha/nf-kappab complex
2RAM 2.4 Å, A novel DNA recognition mode by nf-kb P65 homodimer
1K3Z 2.5 Å, X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex
5U01 2.5 Å, Cooperative DNA binding by two RelA dimers

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