5U01: Cooperative DNA binding by two RelA dimers

Cooperative DNA binding by two RelA dimers. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Synthesium
Chains: 6
Atoms: 10,183
Mol. weight: 140.63 kDa
Released: 27 Sept 2017

Explore 5U01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U01 contains 46 α-helices and 121 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: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	1
β-strand	27	1	2
α-helix	34	1
β-strand	35-36	2	3
α-helix	46-47	2
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	70-77	8	4
β-strand	85	1	4
β-strand	89-92	4	3
β-strand	95-96	2	4
β-strand	99-104	6	4
β-strand	110-112	3	1
β-strand	116-120	5	3
α-helix	121-122	2
α-helix	126-135	10
α-helix	145-148	4
β-strand	156-157	2	5
β-strand	158-166	9	4
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-179	2	4
α-helix	180-182	3
β-strand	183-184	2	5
α-helix	193-194	2
β-strand	196-199	4	6
β-strand	203-205	3	7
β-strand	211-216	6	6
β-strand	220	1	8
β-strand	223	1	8
β-strand	225-230	6	7
β-strand	233-236	4	7
β-strand	238	1	6
α-helix	241-243	3
β-strand	244-245	2	6
β-strand	249-253	5	6
α-helix	254-257	4
β-strand	266-274	9	7
β-strand	279-280	2	7
β-strand	284-289	6	7

Chain B: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	9
α-helix	26	1
β-strand	27	1	10
α-helix	28	1
β-strand	35	1	11
β-strand	48	1	10
β-strand	60-64	5	9
β-strand	71-77	7	12
α-helix	84	1
β-strand	85	1	12
α-helix	86	1
β-strand	89-91	3	11
β-strand	95-96	2	12
β-strand	99-103	5	12
α-helix	104-105	2
β-strand	110-112	3	9
β-strand	117-119	3	11
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
α-helix	145-147	3
β-strand	156-157	2	13
β-strand	158-166	9	12
β-strand	172-174	3	12
α-helix	175-177	3
β-strand	178-179	2	12
β-strand	183-184	2	13
α-helix	189-191	3
β-strand	196-199	4	14
β-strand	203-205	3	15
β-strand	211-216	6	14
β-strand	220	1	16
β-strand	223	1	16
β-strand	225-230	6	15
β-strand	233-236	4	15
β-strand	238	1	14
α-helix	241-243	3
β-strand	244-245	2	14
β-strand	249-253	5	14
α-helix	254-257	4
β-strand	266-274	9	15
β-strand	279-280	2	15
β-strand	284-289	6	15

Chain C: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	17
β-strand	27	1	18
β-strand	35-36	2	19
β-strand	48	1	18
β-strand	55	1	16
β-strand	60-64	5	17
β-strand	70-77	8	20
β-strand	85	1	20
β-strand	89-92	4	19
β-strand	95-96	2	20
β-strand	99-104	6	20
β-strand	110-112	3	17
β-strand	116-120	5	19
α-helix	121-122	2
α-helix	126-135	10
α-helix	145-148	4
β-strand	156-157	2	21
β-strand	158-166	9	20
β-strand	172-174	3	20
α-helix	175-177	3
β-strand	178-179	2	20
α-helix	180-182	3
β-strand	183-184	2	21
β-strand	196-199	4	22
β-strand	203-205	3	23
β-strand	211-216	6	22
β-strand	220	1	24
β-strand	223	1	24
β-strand	225-230	6	23
β-strand	233-236	4	23
β-strand	238	1	22
α-helix	241-243	3
β-strand	244-245	2	22
β-strand	249-253	5	22
α-helix	254-257	4
β-strand	266-274	9	23
β-strand	279-280	2	23
β-strand	284-289	6	23

Chain D: 16 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	25
α-helix	26	1
β-strand	27	1	26
α-helix	28	1
β-strand	35	1	27
α-helix	37-42	6
α-helix	46-47	2
β-strand	48	1	26
β-strand	60-64	5	25
β-strand	71-77	7	28
α-helix	84	1
β-strand	85	1	28
α-helix	86	1
β-strand	89-91	3	27
β-strand	95-96	2	28
β-strand	99-103	5	28
α-helix	104-105	2
β-strand	110-112	3	25
β-strand	117-119	3	27
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
α-helix	145-147	3
β-strand	156-157	2	29
β-strand	158-166	9	28
β-strand	172-174	3	28
α-helix	175-177	3
β-strand	178-179	2	28
β-strand	183-184	2	29
α-helix	189-191	3
α-helix	193-194	2
β-strand	196-199	4	30
β-strand	203-205	3	31
β-strand	211-216	6	30
β-strand	220	1	32
β-strand	223	1	32
β-strand	225-230	6	31
β-strand	233-236	4	31
β-strand	238	1	30
α-helix	241-243	3
β-strand	244-245	2	30
β-strand	249-253	5	30
α-helix	254-257	4
β-strand	266-274	9	31
β-strand	279-280	2	31
β-strand	284-289	6	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor p65	A, B, C, D	protein	273	Mus musculus	Q04207 (AlphaFold model)
DNA (27-mer)	E, F	DNA	27	Synthesium

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

>5U01_1 Transcription factor p65 (chains A, B, C, D)
PYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICR
VNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYA
DPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Sequence of entity 2 (E, F), FASTA

>5U01_2 DNA (27-MER) (chains E, F)
TAGCGGAAATTCCCGGGAATTTCCGCT

Primary citation

DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor kappa B are not correlated. Mulero, M.C., Huang, D.B., Nguyen, H.T. et al. J Biol Chem (2017) 292:18821-18830. DOI 10.1074/jbc.M117.813980 · 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

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