2I9T: NF-kB p65-p50 heterodimer

Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter. Determined by X-ray diffraction at 2.8 Å resolution. Released 6 Feb 2007.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,226
Mol. weight: 77.1 kDa
Released: 6 Feb 2007

Explore 2I9T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2I9T contains 24 α-helices and 56 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: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	1
α-helix	26	1
β-strand	27	1	2
α-helix	28	1
β-strand	35-36	2	3
α-helix	37-39	3
α-helix	45-47	3
β-strand	48	1	2
β-strand	60-62	3	1
β-strand	71-77	7	4
β-strand	85	1	4
β-strand	89-91	3	3
β-strand	95-96	2	4
β-strand	99-103	5	4
α-helix	104-105	2
β-strand	110-112	3	1
β-strand	117-120	4	3
α-helix	124-126	3
α-helix	127-135	9
α-helix	145-147	3
β-strand	156-166	11	4
β-strand	172-174	3	4
β-strand	178-184	7	4
α-helix	193-194	2
β-strand	196-199	4	5
β-strand	205	1	6
β-strand	211-216	6	5
α-helix	221-223	3
β-strand	225-230	6	7
β-strand	233-236	4	7
β-strand	238	1	5
α-helix	241-243	3
β-strand	244-245	2	5
β-strand	249-253	5	5
α-helix	254-257	4
β-strand	266-268	3	8
β-strand	269-274	6	7
β-strand	279-280	2	7
α-helix	281-283	3
β-strand	286-288	3	8
β-strand	289	1	6

Chain B: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	341-346	6	9
β-strand	348	1	10
β-strand	353	1	11
β-strand	356	1	12
α-helix	358-360	3
α-helix	367-368	2
β-strand	369	1	10
β-strand	381-385	5	9
β-strand	391-398	8	13
β-strand	406	1	13
β-strand	410-412	3	12
β-strand	416-417	2	13
β-strand	420-425	6	13
β-strand	433	1	9
β-strand	438-440	3	12
α-helix	444-446	3
α-helix	447-461	15
α-helix	471-473	3
α-helix	488-504	17
β-strand	509-520	12	13
β-strand	524-528	5	13
β-strand	532-538	7	13
β-strand	539	1	11
α-helix	543-545	3
α-helix	547-548	2
β-strand	550-553	4	14
β-strand	557-559	3	15
β-strand	565-570	6	14
α-helix	575-577	3
β-strand	578-585	8	15
β-strand	591-595	5	15
β-strand	597	1	14
α-helix	600-602	3
β-strand	603-604	2	14
β-strand	608-612	5	14
α-helix	613-616	4
β-strand	625-633	9	15
β-strand	639	1	15
β-strand	643-648	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(apgptpgpgpgpapapaptptpcpcptpcptp*g)-3'	C	DNA	17
5'-d(cpapgpapgpgpapaptptptpcpcpcpapcp*t)-3'	D	DNA	17
Transcription factor p65	A	protein	279	Mus musculus	Q04207 (AlphaFold model)
Nuclear factor NF-kappa-B p105 subunit	B	protein	313	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>2I9T_1 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3' (chains C)
AGTGGGAAATTCCTCTG

Sequence of entity 2 (D), FASTA

>2I9T_2 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3' (chains D)
CAGAGGAATTTCCCACT

Sequence of entity 3 (A), FASTA

>2I9T_3 Transcription factor p65 (chains A)
GSHMHAPYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTV
RISLVTKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQ
RIQTNNNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTA
ELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVF
RTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 4 (B), FASTA

>2I9T_4 Nuclear factor NF-kappa-B p105 subunit (chains B)
MGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQL
VTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTE
ACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAF
LPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDD
IQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDL
ETSEPKPFLYYPE

Primary citation

Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter. Escalante, C.R., Shen, L., Thanos, D. et al. Structure (2002) 10:383-391. DOI 10.1016/S0969-2126(02)00723-2 · 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
9BDU 2.03 Å, NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA
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

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