1OOA: Nuclear factor NF-kappa-B p105 subunit

Crystal structure of nf-kB(p50)2 complexed to a high-affinity RNA aptamer. Determined by X-ray diffraction at 2.45 Å resolution. Released 22 Jul 2003.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,442
Mol. weight: 91.96 kDa
Released: 22 Jul 2003

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

Secondary structure: helices and β-sheets

1OOA contains 26 α-helices and 56 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	41-46	6	1
α-helix	47	1
β-strand	48	1	2
α-helix	49	1
β-strand	53	1	3
α-helix	54-55	2
β-strand	56	1	4
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	5
β-strand	106	1	5
β-strand	110-113	4	4
β-strand	116-117	2	5
β-strand	120-125	6	5
β-strand	131-133	3	1
β-strand	137-140	4	4
α-helix	144-146	3
α-helix	147-161	15
α-helix	165-168	4
α-helix	171-173	3
α-helix	188-202	15
β-strand	209-219	11	5
β-strand	225-228	4	5
β-strand	232-238	7	5
β-strand	239	1	3
β-strand	250-253	4	6
β-strand	257-259	3	7
β-strand	265-270	6	6
β-strand	279-285	7	7
β-strand	291-295	5	7
β-strand	297	1	6
α-helix	300-302	3
β-strand	303	1	6
β-strand	308-312	5	6
α-helix	313-316	4
β-strand	325-332	8	7
β-strand	339	1	7
α-helix	340-342	3
β-strand	343-348	6	7

Chain B: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	41-46	6	8
α-helix	47	1
β-strand	48	1	9
α-helix	49	1
β-strand	53	1	10
α-helix	54-55	2
β-strand	56	1	11
α-helix	58-60	3
α-helix	66-68	3
β-strand	69	1	9
β-strand	81-85	5	8
β-strand	92-98	7	12
β-strand	106	1	12
β-strand	110-113	4	11
β-strand	116-117	2	12
β-strand	120-124	5	12
β-strand	131-133	3	8
β-strand	137-140	4	11
α-helix	147-160	14
α-helix	165-168	4
α-helix	171-173	3
α-helix	188-202	15
β-strand	209-219	11	12
β-strand	225-228	4	12
β-strand	232-238	7	12
β-strand	239	1	10
α-helix	242-244	3
β-strand	250-253	4	13
β-strand	257-259	3	14
β-strand	265-270	6	13
β-strand	279-285	7	14
β-strand	291-295	5	14
β-strand	297	1	13
α-helix	300-302	3
β-strand	303	1	13
β-strand	308-312	5	13
α-helix	313-316	4
β-strand	325-332	8	14
β-strand	339	1	14
α-helix	340-342	3
β-strand	343-348	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA aptamer	C, D	RNA	29
Nuclear factor NF-kappa-B p105 subunit	A, B	protein	326	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>1OOA_1 RNA aptamer (chains C, D)
CAUACUUGAAACUGUAAGGUUGGCGUAUG

Sequence of entity 2 (A, B), FASTA

>1OOA_2 Nuclear factor NF-kappa-B p105 subunit (chains A, B)
GGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQL
VTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTE
ACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAF
LPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDD
IQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDL
ETSEPKPFLYYPEIKDKEEVQRKRQK

Primary citation

Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer. Huang, D.B., Vu, D., Cassiday, L.A. et al. Proc Natl Acad Sci U S A (2003) 100:9268-9273. DOI 10.1073/pnas.1632011100 · 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
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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