1LE9: NF-kB heterodimer

Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Apr 2003.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Mus musculus
Chains: 8
Atoms: 10,232
Mol. weight: 146.99 kDa
Released: 15 Apr 2003

Explore 1LE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LE9 contains 34 α-helices and 107 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: 9 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	1
β-strand	30	1	2
β-strand	35	1	3
β-strand	60-62	3	1
β-strand	70-77	8	2
α-helix	84	1
β-strand	85	1	2
α-helix	86	1
β-strand	92	1	4
β-strand	96-97	2	5
β-strand	99	1	5
β-strand	102-104	3	2
β-strand	111-112	2	1
β-strand	116	1	4
β-strand	119	1	3
α-helix	120-122	3
α-helix	127-135	9
α-helix	145-147	3
β-strand	156-165	10	2
β-strand	173-174	2	2
α-helix	175-177	3
β-strand	179-184	6	2
β-strand	196-199	4	6
β-strand	203-205	3	7
β-strand	211-216	6	6
β-strand	220	1	8
β-strand	223	1	8
β-strand	225-228	4	7
β-strand	235-236	2	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
α-helix	281-283	3
β-strand	284-289	6	7

Chain B: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	42-46	5	9
β-strand	48	1	10
β-strand	56	1	11
α-helix	58-60	3
β-strand	69	1	10
β-strand	81-84	4	9
β-strand	91-98	8	12
β-strand	106	1	12
β-strand	110	1	11
β-strand	122-125	4	12
β-strand	133	1	9
β-strand	140	1	11
α-helix	147-156	10
α-helix	187-200	14
β-strand	209-210	2	13
β-strand	211-219	9	12
β-strand	225-233	9	12
β-strand	237-238	2	13
α-helix	247-248	2
β-strand	250-253	4	14
β-strand	257-259	3	15
β-strand	265-270	6	14
β-strand	278-283	6	15
β-strand	293-295	3	15
β-strand	297	1	14
α-helix	300-302	3
β-strand	303-304	2	14
β-strand	308-312	5	14
α-helix	313-316	4
β-strand	325-333	9	15
β-strand	339	1	15
α-helix	340-342	3
β-strand	343-348	6	15

Chain E: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	16
α-helix	26-28	3
β-strand	30-32	3	17
β-strand	36	1	18
β-strand	60-61	2	16
β-strand	71-72	2	19
β-strand	75-76	2	20
α-helix	84-86	3
β-strand	89	1	21
β-strand	111-112	2	16
β-strand	119	1	21
β-strand	120	1	18
α-helix	121-122	2
α-helix	127-134	8
α-helix	145-147	3
β-strand	156	1	17
β-strand	159-161	3	20
β-strand	163-164	2	19
β-strand	174	1	19
β-strand	178-179	2	20
α-helix	180	1
α-helix	182	1
β-strand	184-185	2	17
α-helix	193-194	2
β-strand	196-199	4	22
β-strand	203-205	3	23
β-strand	211-216	6	22
β-strand	220	1	24
β-strand	223	1	24
β-strand	225-228	4	23
β-strand	235-236	2	23
β-strand	238	1	22
α-helix	241-243	3
β-strand	244	1	22
β-strand	249-253	5	22
α-helix	254-257	4
β-strand	266-274	9	23
β-strand	279-280	2	23
α-helix	281-283	3
β-strand	284-289	6	23

Chain F: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	25
α-helix	58-60	3
β-strand	81	1	25
β-strand	91-98	8	26
β-strand	106	1	26
β-strand	110	1	27
β-strand	122-125	4	26
β-strand	133	1	25
β-strand	140	1	27
α-helix	141-143	3
α-helix	146-156	11
α-helix	187-200	14
β-strand	209-210	2	28
β-strand	211-219	9	26
β-strand	225-233	9	26
β-strand	237-238	2	28
α-helix	243-245	3
β-strand	250-253	4	29
β-strand	257-259	3	30
β-strand	265-270	6	29
β-strand	278-283	6	30
β-strand	293-295	3	30
β-strand	297	1	29
β-strand	303-304	2	29
β-strand	308-312	5	29
α-helix	313-316	4
β-strand	325-333	9	30
β-strand	339	1	30
α-helix	340-342	3
β-strand	343-348	6	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(tpgpgpgpapcptptptpcpcpt)-3'	C, G	DNA	12
5'-d(apapgpgpapapapgptpcpcpc)-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

>1LE9_1 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3' (chains C, G)
TGGGACTTTCCT

Sequence of entity 2 (D, H), FASTA

>1LE9_2 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3' (chains D, H)
AAGGAAAGTCCC

Sequence of entity 3 (A, E), FASTA

>1LE9_3 NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT (chains A, E)
MAYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLV
TKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTN
NNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKIC
RVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPY
ADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 4 (B, F), FASTA

>1LE9_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-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B 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

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