1K3Z: IkBb/NF-kB p65 homodimer complex

X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 4 Oct 2002.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,769
Mol. weight: 62.03 kDa
Released: 4 Oct 2002

Explore 1K3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K3Z contains 24 α-helices and 22 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: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	196-199	4	1
β-strand	203-205	3	2
β-strand	211-216	6	1
β-strand	225-230	6	2
β-strand	233-236	4	2
β-strand	238	1	1
α-helix	241-243	3
β-strand	244	1	1
β-strand	249-253	5	1
α-helix	254-257	4
β-strand	266-274	9	2
β-strand	279-280	2	2
α-helix	281-283	3
β-strand	284-289	6	2
α-helix	294-303	10
α-helix	306-312	7

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	196-199	4	3
β-strand	203-205	3	4
β-strand	211-216	6	3
β-strand	225-230	6	4
β-strand	233-236	4	4
β-strand	238	1	3
α-helix	241-243	3
β-strand	244-245	2	3
β-strand	249-253	5	3
α-helix	254-257	4
β-strand	266-273	8	4
β-strand	280	1	4
β-strand	284-289	6	4
α-helix	293-295	3
α-helix	301-304	4

Chain D: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	61-68	8
α-helix	71-81	11
α-helix	97-104	8
α-helix	107-115	9
α-helix	130-137	8
α-helix	140-146	7
α-helix	149-151	3
α-helix	196-199	4
α-helix	210-216	7
α-helix	220-229	10
α-helix	244-250	7
α-helix	254-263	10
α-helix	277-282	6
α-helix	287-296	10
α-helix	304-307	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor p65	A, B	protein	136	Mus musculus	Q04207 (AlphaFold model)
transcription factor inhibitor I-kappa-B-beta	D	protein	282	Mus musculus	Q60778 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1K3Z_1 Transcription factor p65 (chains A, B)
TAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAI
VFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFK
SIMKKSPFNGPTEPRP

Sequence of entity 2 (D), FASTA

>1K3Z_2 transcription factor inhibitor I-kappa-B-beta (chains D)
VFGYVTEDGDTALHLAVIHQHEPFLDFLLGFSAGHEYLDLQNDLGQTALHLAAILGEAST
VEKLYAAGAGVLVAERGGHTALHLACRVRAHTCACVLLQPRPSHPRDASDTYLTQSQDCT
PDTSHAPAAVDSQPNPENEEEPRDEDWRLQLEAENYDGHTPLHVAVIHKDAEMVRLLRDA
GADLNKPEPTCGRTPLHLAVEAQAASVLELLLKAGADPTARMYGGRTPLGSALLRPNPIL
ARLLRAHGAPEPEDGGDKLSPCEEEGEDEDSDNRDEGDEYDD

Primary citation

X-ray crystal structure of an IkappaBbeta x NF-kappaB p65 homodimer complex. Malek, S., Huang, D.B., Huxford, T. et al. J Biol Chem (2003) 278:23094-23100. DOI 10.1074/jbc.M301022200 · 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
5U01 2.5 Å, Cooperative DNA binding by two RelA dimers

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