8TKM: Nuclear factor NF-kappa-B p50 subunit

Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 17-mer kappaB DNA from human interleukin-6 (IL-6) promoter. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Oct 2023.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 5,648
Mol. weight: 80.26 kDa
Released: 11 Oct 2023

Explore 8TKM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TKM contains 25 α-helices and 54 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, 26 β-strands

Element	Residues	Length	Sheet
β-strand	41-46	6	1
α-helix	47	1
β-strand	48	1	2
α-helix	49	1
α-helix	53-55	3
β-strand	56	1	3
α-helix	58-60	3
α-helix	66-68	3
β-strand	69	1	2
β-strand	81-85	5	1
β-strand	91-98	8	4
β-strand	106	1	4
β-strand	110-113	4	3
β-strand	116-117	2	4
β-strand	120-125	6	4
β-strand	131-133	3	1
β-strand	137-140	4	3
α-helix	144-146	3
α-helix	147-161	15
α-helix	165-168	4
α-helix	171-175	5
α-helix	188-202	15
β-strand	209-219	11	4
β-strand	225-228	4	4
α-helix	229-231	3
β-strand	232-238	7	4
α-helix	243-245	3
β-strand	250-253	4	5
β-strand	257-259	3	6
β-strand	265-270	6	5
β-strand	278-285	8	6
β-strand	291-295	5	6
β-strand	297	1	5
α-helix	300-302	3
β-strand	303-304	2	5
β-strand	308-312	5	5
α-helix	313-316	4
β-strand	325-333	9	6
β-strand	339	1	6
β-strand	343-348	6	6

Chain B: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	41-46	6	7
α-helix	47	1
β-strand	48	1	8
α-helix	49	1
β-strand	56	1	9
α-helix	58-60	3
β-strand	69	1	8
β-strand	73	1	10
β-strand	76	1	10
β-strand	81-85	5	7
β-strand	91-98	8	11
β-strand	106	1	11
β-strand	110-113	4	9
β-strand	116-117	2	11
β-strand	120-125	6	11
β-strand	131-133	3	7
β-strand	137-140	4	9
α-helix	147-161	15
α-helix	165-169	5
α-helix	171-176	6
α-helix	188-200	13
β-strand	209-219	11	11
β-strand	225-228	4	11
α-helix	229-231	3
β-strand	232-238	7	11
α-helix	247-248	2
β-strand	250-253	4	12
β-strand	257-259	3	13
β-strand	265-270	6	12
α-helix	275-277	3
β-strand	278-285	8	13
β-strand	291-295	5	13
β-strand	297	1	12
α-helix	300-302	3
β-strand	303-304	2	12
β-strand	308-312	5	12
β-strand	325-333	9	13
β-strand	339	1	13
β-strand	343-348	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear factor NF-kappa-B p50 subunit	A, B	protein	312	Mus musculus	P25799 (AlphaFold model)
17-mer kappaB DNA	C	DNA	17	Homo sapiens
17-mer kappaB DNA	D	DNA	17	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8TKM_1 Nuclear factor NF-kappa-B p50 subunit (chains A, B)
GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLV
TNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEA
CIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFL
PDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDI
QIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLE
TSEPKPFLYYPE

Sequence of entity 2 (C), FASTA

>8TKM_2 17-mer kappaB DNA (chains C)
TGTGGGATTTTCCCATG

Sequence of entity 3 (D), FASTA

>8TKM_3 17-mer kappaB DNA (chains D)
CATGGGAAAATCCCACA

Primary citation

X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA. Zhu, N., Mealka, M., Mitchel, S. et al. Biomolecules (2023) 13. DOI 10.3390/biom13091310 · PubMed

Other PDB entries of the same protein (UniProt P25799 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U36 1.89 Å, Crystal structure of WLAC mutant of dimerisation domain of NF-kB p50 transcription factor
1U3Z 1.9 Å, Crystal structure of MLAC mutant of dimerisation domain of NF-kB p50 transcription factor
1U3J 1.9 Å, Crystal structure of MLAV mutant of dimerisation domain of NF-kB p50 transcription factor
1U3Y 1.9 Å, Crystal structure of ILAC mutant of dimerisation domain of NF-kB p50 transcription factor
9BOR 2.0 Å, IkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex at 2.0 Angstrom…
1BFS 2.2 Å, Structure of nf-kb P50 homodimer bound to a kb site
1U41 2.2 Å, Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor
1IKN 2.3 Å, Ikappabalpha/nf-kappab complex
1NFK 2.3 Å, Structure of the nuclear factor kappa-B (nf-kb) P50 homodimer
1OOA 2.45 Å, Crystal structure of nf-kB(p50)2 complexed to a high-affinity RNA aptamer
1U42 2.7 Å, Crystal structure of MLAM mutant of dimerisation domain of NF-kB p50 transcription factor
1LEI 2.7 Å, The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV…

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