5YBD: ETS domain of Ergp55

X-ray structure of ETS domain of Ergp55 in complex with E74DNA. Determined by X-ray diffraction at 2.77 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 2.77 Å
Organisms: Homo sapiens, Drosophila saltans, Drosophila adunca
Chains: 6
Atoms: 2,379
Mol. weight: 34.82 kDa
Released: 14 Nov 2018

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

Secondary structure: helices and β-sheets

5YBD contains 10 α-helices and 8 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	313-322	10
α-helix	324-326	3
β-strand	331-332	2	1
β-strand	338-340	3	1
α-helix	344-355	12
α-helix	362-374	13
β-strand	378-380	3	1
β-strand	387-390	4	1
α-helix	392-405	14

Chain X: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	313-322	10
α-helix	324-326	3
β-strand	331-332	2	2
β-strand	338-340	3	2
α-helix	344-355	12
α-helix	362-374	13
β-strand	378-380	3	2
β-strand	387-390	4	2
α-helix	392-400	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional regulator ERG	A, X	protein	97	Homo sapiens	P11308 (AlphaFold model)
DNA (5'-d(papcpcpgpgpapapgp*t)-3')	B, Y	DNA	9	Drosophila saltans
DNA (5'-d(pcpapcptptpcpcpgpgpt)-3')	C, Z	DNA	10	Drosophila adunca

Sequence of entity 1 (A, X), FASTA

>5YBD_1 Transcriptional regulator ERG (chains A, X)
QIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRAL
RYYYDKNIMTKVHGKRYAYKFDFHGIAQALLEHHHHH

Sequence of entity 2 (B, Y), FASTA

>5YBD_2 DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3') (chains B, Y)
ACCGGAAGT

Sequence of entity 3 (C, Z), FASTA

>5YBD_3 DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3') (chains C, Z)
CACTTCCGGT

Primary citation

Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence. Sharma, R., Gangwar, S.P., Saxena, A.K. Acta Crystallogr F Struct Biol Commun (2018) 74:656-663. DOI 10.1107/S2053230X1801110X · PubMed

Other PDB entries of the same protein (UniProt P11308 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IRG 1.7 Å, Uninhibited DNA-binding domain of the Ets transcription factor ERG
4IRH 2.1 Å, Auto-inhibited ERG Ets domain
5YBC 2.5 Å, X-ray structure of native ETS-domain domain of Ergp55
4IRI 2.77 Å, Auto-inhibited ERG Ets Domain-DNA Complex
6VGE 4.25 Å, Crystal structure of the DNA binding domains of human transcription factor ERG, human…
6VGG 4.31 Å, Crystal structure of the DNA binding domains of human transcription factor ERG, human…
1SXE The solution structure of the Pointed (PNT) domain from the transcrition factor Erg

Browse structure collections

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