2RAM: Protein

A novel DNA recognition mode by nf-kb P65 homodimer. Determined by X-ray diffraction at 2.4 Å resolution. Released 27 May 1998.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,314
Mol. weight: 75.05 kDa
Ligands: DTV
Released: 27 May 1998

Explore 2RAM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RAM contains 27 α-helices and 57 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: 15 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	1
α-helix	26	1
β-strand	27	1	2
α-helix	28	1
α-helix	32-34	3
β-strand	35-36	2	3
α-helix	46-47	2
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	71-78	8	4
α-helix	84	1
β-strand	85	1	4
α-helix	86	1
β-strand	89-91	3	3
β-strand	95-96	2	4
β-strand	99-103	5	4
α-helix	104-105	2
β-strand	110-112	3	1
β-strand	117-120	4	3
α-helix	121-122	2
α-helix	126-135	10
β-strand	156-166	11	4
β-strand	172-174	3	4
β-strand	178-179	2	4
α-helix	181-182	2
β-strand	183-184	2	4
α-helix	192-194	3
β-strand	196-199	4	5
β-strand	203-205	3	6
β-strand	211-216	6	5
β-strand	225-230	6	6
β-strand	233-236	4	6
β-strand	238	1	5
α-helix	241-243	3
β-strand	244	1	5
β-strand	249-253	5	5
α-helix	254-256	3
β-strand	266-274	9	6
α-helix	275-277	3
β-strand	279-280	2	6
α-helix	281-283	3
β-strand	284-289	6	6

Chain B: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	7
α-helix	26	1
β-strand	27	1	8
α-helix	28	1
α-helix	33-34	2
β-strand	35-36	2	9
α-helix	37-39	3
α-helix	46-47	2
β-strand	48	1	8
β-strand	60-64	5	7
β-strand	70-77	8	10
β-strand	85	1	10
β-strand	89-91	3	9
β-strand	95-96	2	10
β-strand	99-102	4	10
β-strand	110-112	3	7
β-strand	117-120	4	9
α-helix	126-135	10
β-strand	156-157	2	11
β-strand	158-166	9	10
β-strand	172-174	3	10
α-helix	175-177	3
β-strand	178-179	2	10
α-helix	180-181	2
β-strand	183-184	2	11
α-helix	193-194	2
β-strand	196-199	4	12
β-strand	203-205	3	13
β-strand	211-216	6	12
β-strand	220	1	14
β-strand	223	1	14
β-strand	225-230	6	13
β-strand	233-236	4	13
β-strand	238	1	12
α-helix	241-243	3
β-strand	244-245	2	12
β-strand	249-253	5	12
α-helix	254-256	3
β-strand	266-274	9	13
β-strand	279-280	2	13
α-helix	281-283	3
β-strand	284-289	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-D(CPGPGPCPTPGPGPAPAPAPTP(5IU)P(5IU)PCPCPAPGPCPCPG)-3')	C, D	DNA	20
Protein (transcription factor nf-kb P65)	A, B	protein	273	Mus musculus	Q04207 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>2RAM_1 DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3') (chains C, D)
CGGCTGGAAATUUCCAGCCG

Sequence of entity 2 (A, B), FASTA

>2RAM_2 PROTEIN (TRANSCRIPTION FACTOR NF-KB P65) (chains A, B)
PYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRAPNTAELKICR
VNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYA
DPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPD

Ligands and cofactors

ID	Name	Formula	Copies
DTV	(2S,3S)-1,4-dimercaptobutane-2,3-diol	C4 H10 O2 S2	2

Primary citation

A novel DNA recognition mode by the NF-kappa B p65 homodimer. Chen, Y.Q., Ghosh, S., Ghosh, G. Nat Struct Biol (1998) 5:67-73. DOI 10.1038/nsb0198-67 · 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
1K3Z 2.5 Å, X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex
5U01 2.5 Å, Cooperative DNA binding by two RelA dimers

Browse structure collections

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