1LEI: Nuclear factor nf-kappa-B P65 subunit

The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription. Determined by X-ray diffraction at 2.7 Å resolution. Released 15 Apr 2003.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,344
Mol. weight: 77.03 kDa
Released: 15 Apr 2003

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

Secondary structure: helices and β-sheets

1LEI contains 22 α-helices and 53 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: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	1
α-helix	26-28	3
α-helix	32-34	3
β-strand	35	1	2
β-strand	60-64	5	1
β-strand	71-77	7	3
α-helix	84	1
β-strand	85	1	3
α-helix	86	1
β-strand	89-91	3	2
β-strand	95-96	2	3
β-strand	99-103	5	3
β-strand	110-112	3	1
β-strand	117-119	3	2
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-134	9
α-helix	145-147	3
β-strand	156-166	11	3
β-strand	172-174	3	3
α-helix	175-177	3
β-strand	178-184	7	3
α-helix	193-194	2
β-strand	196-199	4	4
β-strand	203-205	3	5
β-strand	211-216	6	4
α-helix	221-223	3
β-strand	225-230	6	5
β-strand	233-236	4	5
β-strand	238	1	4
α-helix	241-243	3
β-strand	244-245	2	4
β-strand	249-253	5	4
α-helix	254-257	4
β-strand	266-274	9	5
β-strand	279-280	2	5
α-helix	281-283	3
β-strand	284-289	6	5

Chain B: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	6
β-strand	48	1	7
β-strand	53	1	8
β-strand	56-57	2	9
β-strand	69	1	7
β-strand	81-84	4	6
β-strand	92-98	7	10
β-strand	106	1	10
β-strand	110-111	2	9
β-strand	116-117	2	10
β-strand	120-124	5	10
β-strand	131-133	3	6
β-strand	139-141	3	9
α-helix	142-143	2
α-helix	146-156	11
α-helix	171-173	3
α-helix	190-202	13
β-strand	209-210	2	11
β-strand	211-218	8	10
β-strand	227-233	7	10
α-helix	235-236	2
β-strand	237-238	2	11
β-strand	239	1	8
α-helix	247-248	2
β-strand	250-253	4	12
β-strand	257-259	3	13
β-strand	265-270	6	12
β-strand	279-284	6	13
β-strand	292-295	4	13
β-strand	297	1	12
α-helix	300-302	3
β-strand	303-304	2	12
β-strand	308-312	5	12
α-helix	313-316	4
β-strand	325-332	8	13
β-strand	339	1	13
β-strand	343-348	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(cptpcpapgpgpgpapapapgptpapcpapgp*a)-3'	C	DNA	17
5'-D(TPCPTPGP5ITPAPCP5ITP5ITP5ITPCPCPCPTPGPAP*G)-3'	D	DNA	17
Nuclear factor nf-kappa-B P65 subunit	A	protein	274	Mus musculus	Q04207 (AlphaFold model)
Nuclear factor nf-kappa-B P50 subunit	B	protein	313	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1LEI_1 5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3' (chains C)
CTCAGGGAAAGTACAGA

Sequence of entity 2 (D), FASTA

>1LEI_2 5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3' (chains D)
TCTGUACUUUCCCTGAG

Sequence of entity 3 (A), FASTA

>1LEI_3 NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT (chains A)
MAYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLV
TKDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTN
NNPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKIC
RVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPY
ADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 4 (B), FASTA

>1LEI_4 NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT (chains B)
MGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQL
VTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTE
ACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAF
LPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDD
IQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDL
ETSEPKPFLYYPE

Primary citation

The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription. Chen-Park, F.E., Huang, D.B., Noro, B. et al. J Biol Chem (2002) 277:24701-24708. DOI 10.1074/jbc.M200007200 · 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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