1NFK: Nuclear factor kappa-B (nf-kb) P50 homodimer

Structure of the nuclear factor kappa-B (nf-kb) P50 homodimer. Determined by X-ray diffraction at 2.3 Å resolution. Released 23 Dec 1996.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,667
Mol. weight: 79.89 kDa
Released: 23 Dec 1996

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

Secondary structure: helices and β-sheets

1NFK contains 22 α-helices and 59 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: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	41-44	4	1
α-helix	47	1
β-strand	48	1	2
α-helix	49	1
β-strand	56	1	3
α-helix	58-60	3
α-helix	67-68	2
β-strand	69	1	2
β-strand	81-85	5	1
β-strand	92-98	7	4
β-strand	106	1	4
β-strand	110-112	3	3
β-strand	116-117	2	4
β-strand	120-124	5	4
β-strand	131-133	3	1
β-strand	138-140	3	3
α-helix	141-143	3
α-helix	147-160	14
α-helix	165-169	5
α-helix	185-187	3
α-helix	188-203	16
β-strand	209-210	2	5
β-strand	211-219	9	4
β-strand	225-228	4	4
α-helix	229-231	3
β-strand	232-233	2	4
β-strand	237-238	2	5
β-strand	250-253	4	6
β-strand	258-259	2	7
β-strand	265-270	6	6
β-strand	278-284	7	7
β-strand	292-295	4	7
β-strand	297	1	6
α-helix	300-302	3
β-strand	303	1	6
β-strand	308-312	5	6
α-helix	313-315	3
β-strand	325-333	9	7
β-strand	339	1	7
α-helix	340-342	3
β-strand	343-348	6	7

Chain B: 9 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	41-44	4	8
β-strand	48	1	9
β-strand	53	1	10
α-helix	54-55	2
β-strand	56-57	2	11
α-helix	58-60	3
β-strand	69	1	9
β-strand	81-85	5	8
β-strand	91-98	8	12
β-strand	106	1	12
β-strand	110-112	3	11
β-strand	116-117	2	12
β-strand	120-125	6	12
β-strand	131-133	3	8
β-strand	138-141	4	11
α-helix	142-143	2
α-helix	147-159	13
α-helix	165-168	4
α-helix	171-173	3
α-helix	189-204	16
β-strand	209-210	2	13
β-strand	211-217	7	12
β-strand	218	1	14
β-strand	227	1	14
β-strand	232-233	2	12
β-strand	237-238	2	13
β-strand	239	1	10
β-strand	250-253	4	15
β-strand	257-259	3	16
β-strand	265-270	6	15
β-strand	279-283	5	16
β-strand	293-295	3	16
β-strand	297	1	15
α-helix	300-302	3
β-strand	303	1	15
β-strand	308-312	5	15
α-helix	313-315	3
β-strand	325-332	8	16
β-strand	339	1	16
β-strand	343-348	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(tpgpgpgpapaptptpcpcp*c)-3')	C, D	DNA	11
Protein (nuclear factor kappa-B (nf-kb))	A, B	protein	325	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>1NFK_1 DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3') (chains C, D)
TGGGAATTCCC

Sequence of entity 2 (A, B), FASTA

>1NFK_2 PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB)) (chains A, B)
GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLV
TNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEA
CIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFL
PDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDI
QIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLE
TSEPKPFLYYPEIKDKEEVQRKRQK

Primary citation

Structure of NF-kappa B p50 homodimer bound to a kappa B site. Ghosh, G., van Duyne, G., Ghosh, S. et al. Nature (1995) 373:303-310. DOI 10.1038/373303a0 · 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
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…
1LE5 2.75 Å, Crystal structure of a NF-kB heterodimer bound to an IFNb-kB

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