6X6E: Glucocorticoid Receptor DNA binding domain

Glucocorticoid Receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-GBS). Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Jun 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,878
Mol. weight: 28.1 kDa
Ligands: ZN
Released: 2 Jun 2021

Explore 6X6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X6E contains 7 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: 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	474-484	11

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	420	1	3
β-strand	427	1	3
α-helix	428	1
β-strand	430-432	3	4
β-strand	435-437	3	4
α-helix	439-449	11
α-helix	469-471	3
α-helix	474-483	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucocorticoid receptor	A, B	protein	75	Homo sapiens	P04150 (AlphaFold model)
DNA (5'-D(CPCPAPGPAPAPCPGPGPAPGP(5CM)PGPTPTPCPTPG)-3')	C	DNA	18	Homo sapiens
DNA (5'-D(TPCPAPGPAPAPCPGPCPTPCP(5CM)PGPTPTPCPTPG)-3')	D	DNA	18	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6X6E_1 Glucocorticoid receptor (chains A, B)
PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPAC
RYRKCLQAGMNLEAR

Sequence of entity 2 (C), FASTA

>6X6E_2 DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*(5CM)P*GP*TP*TP*CP*TP*G)-3') (chains C)
CCAGAACGGAGCGTTCTG

Sequence of entity 3 (D), FASTA

>6X6E_3 DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*(5CM)P*GP*TP*TP*CP*TP*G)-3') (chains D)
TCAGAACGCTCCGTTCTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. Liu, X., Weikum, E.R., Tilo, D. et al. Nucleic Acids Res (2021) 49:8923-8933. DOI 10.1093/nar/gkab605 · 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
5CBX 2.0 Å, AncGR DNA Binding Domain - (+)GRE Complex
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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