1LE5: NF-kB heterodimer

Crystal structure of a NF-kB heterodimer bound to an IFNb-kB. Determined by X-ray diffraction at 2.75 Å resolution. Released 15 Apr 2003.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Mus musculus
Chains: 8
Atoms: 10,439
Mol. weight: 146.99 kDa
Released: 15 Apr 2003

Explore 1LE5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LE5 contains 38 α-helices and 113 β-strands across 4 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: 10 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	1
β-strand	27	1	2
β-strand	30	1	3
β-strand	35	1	4
β-strand	48	1	2
β-strand	60-61	2	5
β-strand	63-64	2	1
β-strand	71	1	6
β-strand	74-77	4	7
α-helix	84	1
β-strand	85	1	7
α-helix	86	1
β-strand	90-91	2	8
β-strand	111-112	2	5
β-strand	117-118	2	8
β-strand	119	1	4
α-helix	126-134	9
β-strand	156-157	2	3
β-strand	158-161	4	7
β-strand	164-166	3	6
β-strand	172-174	3	6
β-strand	178-179	2	7
α-helix	180	1
α-helix	182	1
β-strand	183-184	2	3
β-strand	196-199	4	9
β-strand	205	1	10
β-strand	211-216	6	9
α-helix	221-223	3
β-strand	225-228	4	11
β-strand	235-236	2	11
β-strand	238	1	9
α-helix	241-243	3
β-strand	244-245	2	9
β-strand	249-253	5	9
α-helix	254-257	4
β-strand	266-274	9	11
β-strand	279-280	2	11
α-helix	281-283	3
β-strand	284-288	5	11
β-strand	289	1	10
α-helix	290	1

Chain B: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	12
β-strand	57	1	13
α-helix	58-60	3
β-strand	81-83	3	12
β-strand	92-98	7	14
β-strand	106	1	14
β-strand	110-112	3	15
β-strand	116-117	2	14
β-strand	119	1	15
β-strand	120-123	4	14
β-strand	131-133	3	12
β-strand	138-140	3	15
β-strand	141	1	13
α-helix	142-143	2
α-helix	146-157	12
α-helix	191-204	14
β-strand	211-217	7	14
β-strand	228-236	9	14
α-helix	243-245	3
β-strand	250-253	4	16
β-strand	257-259	3	17
β-strand	265-270	6	16
α-helix	275-277	3
β-strand	279-285	7	17
β-strand	291-295	5	17
β-strand	297	1	16
α-helix	300-302	3
β-strand	303-304	2	16
β-strand	308-312	5	16
α-helix	313-316	4
β-strand	325-332	8	17
β-strand	339	1	17
β-strand	343-348	6	17

Chain E: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	18
β-strand	27	1	19
β-strand	35	1	20
α-helix	46-47	2
β-strand	48	1	19
β-strand	60	1	21
β-strand	61	1	18
β-strand	71-77	7	22
α-helix	84	1
β-strand	85	1	22
α-helix	86	1
β-strand	89-92	4	20
β-strand	112	1	21
β-strand	116-119	4	20
α-helix	123-125	3
α-helix	127-134	8
α-helix	145-147	3
β-strand	156-157	2	23
β-strand	158-166	9	22
β-strand	172-174	3	22
α-helix	175-177	3
β-strand	178-179	2	22
β-strand	183-184	2	23
α-helix	193-194	2
β-strand	196-199	4	24
β-strand	205	1	25
β-strand	211-216	6	24
α-helix	221-223	3
β-strand	225-228	4	26
β-strand	235-236	2	26
β-strand	238	1	24
β-strand	244-245	2	24
β-strand	249-253	5	24
α-helix	254-257	4
β-strand	266-274	9	26
β-strand	279-280	2	26
α-helix	281-283	3
β-strand	284-288	5	26
β-strand	289	1	25
α-helix	290	1

Chain F: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	41-44	4	27
β-strand	48	1	28
β-strand	53	1	29
β-strand	56-57	2	30
α-helix	58-60	3
β-strand	69	1	28
β-strand	81-85	5	27
β-strand	92-98	7	31
β-strand	106	1	31
β-strand	110-113	4	30
β-strand	116-117	2	31
β-strand	119	1	30
β-strand	120-123	4	31
β-strand	131-133	3	27
β-strand	137-141	5	30
α-helix	142-143	2
α-helix	146-157	12
α-helix	171-174	4
α-helix	191-200	10
β-strand	211-217	7	31
β-strand	228-236	9	31
β-strand	239	1	29
β-strand	250-253	4	32
β-strand	257-259	3	33
β-strand	265-270	6	32
α-helix	275-277	3
β-strand	279-285	7	33
β-strand	291-295	5	33
β-strand	297	1	32
α-helix	300-302	3
β-strand	303-304	2	32
β-strand	308-312	5	32
α-helix	313-316	4
β-strand	325-332	8	33
β-strand	339	1	33
β-strand	343-348	6	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(tpgpgpgpapapaptptpcpcpt)-3'	C, G	DNA	12
5'-d(apapgpgpapaptptptpcpcpc)-3'	D, H	DNA	12
Nuclear factor NF-kappa-B p65 subunit	A, E	protein	274	Mus musculus	Q04207 (AlphaFold model)
Nuclear factor NF-kappa-B p50 subunit	B, F	protein	313	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C, G), FASTA

>1LE5_1 5'-D(*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*T)-3' (chains C, G)
TGGGAAATTCCT

Sequence of entity 2 (D, H), FASTA

>1LE5_2 5'-D(*AP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3' (chains D, H)
AAGGAATTTCCC

Sequence of entity 3 (A, E), FASTA

>1LE5_3 Nuclear factor NF-kappa-B p65 subunit (chains A, E)
MAYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLV
TKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTN
NNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKIC
RVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPY
ADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 4 (B, F), FASTA

>1LE5_4 Nuclear factor NF-kappa-B p50 subunit (chains B, F)
MGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQL
VTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTE
ACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAF
LPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDD
IQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDL
ETSEPKPFLYYPE

Primary citation

The X-ray crystal structure of the NF-kB p50/p65 heterodimer bound to the Interferon beta-kB site. Berkowitz, B., Huang, D.B., Chen-Park, F.E. et al. J Biol Chem (2002) 277:24694-24700. DOI 10.1074/jbc.M200006200 · 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

Browse structure collections

About this viewer

MolViewer shows 1LE5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.