1U41: Nuclear factor NF-kappa-B p105 subunit

Name: PDB 1U41: Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor
Published: 2004-08-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Aug 2004.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 3,691
Mol. weight: 48.97 kDa
Released: 17 Aug 2004

Explore 1U41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1U41 contains 11 α-helices and 45 β-strands across 4 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	1
β-strand	257-259	3	2
β-strand	265-270	6	1
β-strand	281-286	6	2
β-strand	290-295	6	2
β-strand	297	1	1
α-helix	300-302	3
β-strand	303	1	1
β-strand	308-312	5	1
α-helix	313-316	4
β-strand	325-330	6	2
β-strand	332	1	3
β-strand	339	1	3
α-helix	340-342	3
β-strand	343-348	6	2

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	4
β-strand	257-259	3	5
β-strand	265-270	6	4
β-strand	279-285	7	5
β-strand	291-295	5	5
β-strand	297	1	4
α-helix	300-302	3
β-strand	303	1	4
β-strand	308-312	5	4
α-helix	313-316	4
β-strand	325-332	8	5
β-strand	339	1	5
β-strand	343-348	6	5

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	6
β-strand	257-259	3	7
β-strand	265-270	6	6
β-strand	278-283	6	7
β-strand	293-295	3	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	325-333	9	7
β-strand	339	1	7
α-helix	340-342	3
β-strand	343-348	6	7

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	250-253	4	8
β-strand	257-259	3	9
β-strand	265-270	6	8
β-strand	279-285	7	9
β-strand	291-295	5	9
β-strand	297	1	8
α-helix	300-302	3
β-strand	303-304	2	8
β-strand	308-312	5	8
α-helix	313-316	4
β-strand	325-332	8	9
β-strand	339	1	9
α-helix	340-342	3
β-strand	343-348	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear factor NF-kappa-B p105 subunit	A, B, C, D	protein	106	Mus musculus	P25799 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1U41_1 Nuclear factor NF-kappa-B p105 subunit (chains A, B, C, D)
ASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVH
RQFGIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPE

Primary citation

Snapshot of Protein Structure Evolution Reveals Conservation of Functional Dimerization through Intertwined Folding. Chirgadze, D.Y., Demydchuk, M., Becker, M. et al. Structure (2004) 12:1489-1494. DOI 10.1016/j.str.2004.06.011 · 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
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…
1LE5 2.75 Å, Crystal structure of a NF-kB heterodimer bound to an IFNb-kB

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