1VKX: Protein

Crystal structure of the nfkb P50/P65 heterodimer complexed to the immunoglobulin kb DNA. Determined by X-ray diffraction at 2.9 Å resolution. Released 9 Dec 1998.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,116
Mol. weight: 73.23 kDa
Released: 9 Dec 1998

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

Secondary structure: helices and β-sheets

1VKX contains 16 α-helices and 74 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: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	1
β-strand	23-25	3	2
β-strand	27	1	3
β-strand	30	1	4
β-strand	35-36	2	5
β-strand	48	1	3
β-strand	60-62	3	2
β-strand	64	1	1
β-strand	71-73	3	6
β-strand	76-77	2	7
α-helix	84	1
β-strand	85	1	7
α-helix	86	1
β-strand	89-91	3	5
β-strand	95-96	2	8
β-strand	99-100	2	8
β-strand	103	1	6
β-strand	110-112	3	2
β-strand	117-120	4	5
α-helix	123-125	3
α-helix	126-135	10
α-helix	145-148	4
β-strand	156-157	2	4
β-strand	158-159	2	7
β-strand	160-161	2	9
β-strand	162-166	5	6
β-strand	172-174	3	6
α-helix	175-177	3
β-strand	178-179	2	9
β-strand	183-184	2	4
β-strand	198-199	2	10
β-strand	210-211	2	11
β-strand	214-215	2	10
β-strand	225-226	2	12
β-strand	227-229	3	13
β-strand	234-236	3	13
α-helix	237	1
β-strand	238	1	11
α-helix	241-243	3
β-strand	245	1	14
β-strand	249	1	14
β-strand	250	1	10
β-strand	253-254	2	11
α-helix	255-257	3
β-strand	269	1	13
β-strand	270	1	15
β-strand	272-273	2	12
β-strand	280	1	12
β-strand	284	1	15

Chain B: 7 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	343-346	4	16
β-strand	348	1	17
β-strand	351	1	18
β-strand	356-357	2	19
β-strand	369	1	17
β-strand	381-383	3	16
β-strand	391-395	5	20
β-strand	397-398	2	18
β-strand	406	1	18
β-strand	411-413	3	21
β-strand	416	1	20
β-strand	421-425	5	20
β-strand	431-433	3	16
β-strand	437-439	3	21
β-strand	440-441	2	19
α-helix	444-446	3
α-helix	447-459	13
α-helix	471-473	3
α-helix	488-495	8
α-helix	497-500	4
β-strand	509-512	4	18
β-strand	515-518	4	20
β-strand	527-529	3	20
β-strand	536-538	3	18
α-helix	543-545	3
β-strand	557-559	3	22
β-strand	561	1	23
β-strand	565-569	5	24
β-strand	578	1	25
β-strand	581-585	5	26
β-strand	591-594	4	26
β-strand	597	1	24
α-helix	600-602	3
β-strand	603-604	2	24
β-strand	608-612	5	24
β-strand	615	1	23
β-strand	625	1	22
β-strand	628-630	3	26
β-strand	633	1	25
β-strand	643-644	2	26
β-strand	646-648	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(tpgpgpgpgpapcptptptpcpc)-3')	C	DNA	12
DNA (5'-d(apgpgpapapapgptpcpcpcpc)-3')	D	DNA	12
Protein (nf-kappa B P65 subunit)	A	protein	273	Mus musculus	Q04207 (AlphaFold model)
Protein (nf-kappa B P50 subunit)	B	protein	312	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1VKX_1 DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3') (chains C)
TGGGGACTTTCC

Sequence of entity 2 (D), FASTA

>1VKX_2 DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3') (chains D)
AGGAAAGTCCCC

Sequence of entity 3 (A), FASTA

>1VKX_3 PROTEIN (NF-KAPPA B P65 SUBUNIT) (chains A)
AYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICR
VNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYA
DPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 4 (B), FASTA

>1VKX_4 PROTEIN (NF-KAPPA B P50 SUBUNIT) (chains B)
GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLV
TNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEA
CIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFL
PDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDI
QIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLE
TSEPKPFLYYPE

Primary citation

Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Chen, F.E., Huang, D.B., Chen, Y.Q. et al. Nature (1998) 391:410-413. DOI 10.1038/34956 · 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

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