5CBX: AncGR DNA Binding Domain - (+)GRE Complex

AncGR DNA Binding Domain - (+)GRE Complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: unclassified, synthetic construct
Chains: 8
Atoms: 3,869
Mol. weight: 69.5 kDa
Ligands: ZN
Released: 23 Dec 2015

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

Secondary structure: helices and β-sheets

5CBX contains 10 α-helices and 16 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.

Chains A and E: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	420	1	1
β-strand	427	1	1
α-helix	428	1
β-strand	430-432	3	2
β-strand	435-437	3	2
α-helix	439-450	12
α-helix	474-483	10

Chains B and F: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	420	1	3
β-strand	427	1	3
β-strand	430-432	3	4
β-strand	435-437	3	4
α-helix	439-450	12
α-helix	474-483	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AncGR DNA Binding Domain	A, B, E, F	protein	105	unclassified	P04150 (AlphaFold model)
DNA (5'-d(cpcpapgpapapcpapgpapgptpgptptpcptpg)-3')	C, H	DNA	18	synthetic construct
DNA (5'-d(tpcpapgpapapcpapcptpcptpgptptpcptpg)-3')	D, G	DNA	18	synthetic construct

Sequence of entity 1 (A, B, E, F), FASTA

>5CBX_1 AncGR DNA Binding Domain (chains A, B, E, F)
MHHHHHHSSGVDLGTENLYFQSNAGPPPKICLVCGDEASGCHYGVLTCGSCKVFFKRAVE
GQHNYLCAGRNDCIIDKIRRKNCPACRFRKCLQAGMNLEARKTKK

Sequence of entity 2 (C, H), FASTA

>5CBX_2 DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') (chains C, H)
CCAGAACAGAGTGTTCTG

Sequence of entity 3 (D, G), FASTA

>5CBX_3 DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') (chains D, G)
TCAGAACACTCTGTTCTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Hudson, W.H., Kossmann, B.R., de Vera, I.M. et al. Proc Natl Acad Sci U S A (2016) 113:326-331. DOI 10.1073/pnas.1518960113 · PubMed

Other PDB entries of the same protein (UniProt P04150 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDD 1.8 Å, GR in complex with desisobutyrylciclesonide
5E69 1.85 Å, Glucocorticoid receptor DNA binding domain - IL8 NF-kB response element complex
4HN5 1.9 Å, GR DNA Binding Domain - TSLP nGRE Complex
4P6W 1.95 Å, Crystal Structure of mometasone furoate-bound glucocorticoid receptor ligand binding…
8A9G 1.96 Å, Binary complex of 14-3-3 zeta Glucocorticoid Receptor (GR) pT524 peptide stabilised by…
5CBY 2.0 Å, AncGR2 DNA Binding Domain - (+)GRE Complex
6X6E 2.0 Å, Glucocorticoid Receptor DNA binding domain in complex with methylated precursor for a…
5UC3 2.01 Å, Structure of the dominant negative mutant Glucocorticoid Receptor alpha (L733K/N734P)…
6YMO 2.02 Å, Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pS617 peptide
6YO8 2.09 Å, Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pT524 peptide
3K22 2.1 Å, Glucocorticoid Receptor with Bound alaninamide 10 with TIF2 peptide
5NFP 2.1 Å, Glucocorticoid Receptor in complex with budesonide

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