1IKN: Ikappabalpha/nf-kappab complex

Ikappabalpha/nf-kappab complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Apr 1999.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,979
Mol. weight: 72.77 kDa
Released: 12 Apr 1999

Explore 1IKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IKN contains 27 α-helices and 39 β-strands across 3 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, 29 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
α-helix	32-34	3
β-strand	35-36	2	3
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	71-77	7	4
β-strand	85	1	4
β-strand	89-91	3	3
β-strand	95-97	3	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	121-122	2
α-helix	123-125	3
α-helix	126-135	10
β-strand	156-157	2	5
β-strand	158-166	9	4
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-179	2	4
α-helix	180-182	3
β-strand	183-184	2	5
β-strand	196-199	4	6
β-strand	203-205	3	7
β-strand	211-216	6	6
β-strand	225-230	6	8
β-strand	233-236	4	8
β-strand	238	1	6
α-helix	241-243	3
β-strand	244	1	6
β-strand	249-253	5	6
α-helix	254-257	4
β-strand	266-270	5	7
β-strand	271-273	3	8
β-strand	280	1	8
β-strand	284-289	6	7

Chain C: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	9
β-strand	257-259	3	10
β-strand	265-270	6	9
β-strand	278-285	8	10
β-strand	291-295	5	10
α-helix	300-302	3
β-strand	303-304	2	9
β-strand	308-312	5	9
α-helix	313-316	4
β-strand	325-333	9	10
β-strand	339	1	10
β-strand	343-348	6	10

Chain D: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	79-83	5
α-helix	114-120	7
α-helix	124-128	5
α-helix	147-154	8
α-helix	157-165	9
α-helix	175-177	3
α-helix	186-192	7
α-helix	196-205	10
α-helix	220-226	7
α-helix	230-237	8
α-helix	253-256	4
α-helix	263-270	8
α-helix	275-277	3
α-helix	280-281	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (nf-kappa-B P65 subunit)	A	protein	286	Mus musculus	Q04207 (AlphaFold model)
Protein (nf-kappa-B P50D subunit)	C	protein	119	Mus musculus	P25799 (AlphaFold model)
Protein (I-kappa-B-alpha)	D	protein	236	Homo sapiens	P25963 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1IKN_1 PROTEIN (NF-KAPPA-B P65 SUBUNIT) (chains A)
PYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICR
VNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYA
DPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKR

Sequence of entity 2 (C), FASTA

>1IKN_2 PROTEIN (NF-KAPPA-B P50D SUBUNIT) (chains C)
ASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVH
RQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQK

Sequence of entity 3 (D), FASTA

>1IKN_3 PROTEIN (I-KAPPA-B-ALPHA) (chains D)
KQQLTEDGDSFLHLAIIHEEKALTMEVIRQVKGDLAFLNFQNNLQQTPLHLAVITNQPEI
AEALLGAGCDPELRDFRGNTPLHLACEQGCLASVGVLTQSCTTPHLHSILKATNYNGHTC
LHLASIHGYLGIVELLVSLGADVNAQEPCNGRTALHLAVDLQNPDLVSLLLKCGADVNRV
TYQGYSPYQLTWGRPSTRIQQQLGQLTLENLQMLPESEDEESYDTESEFTEFTEDE

Primary citation

The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation. Huxford, T., Huang, D.B., Malek, S. et al. Cell (1998) 95:759-770. DOI 10.1016/S0092-8674(00)81699-2 · 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
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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