6YGJ: 14-3-3 protein beta/alpha

small-molecule stabilizer of 14-3-3 and the Carbohydrate Response Element Binding Protein (ChREBP) protein-protein interaction. Determined by X-ray diffraction at 2.07 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,114
Mol. weight: 59.14 kDa
Ligands: OQE
Released: 16 Sept 2020

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

Secondary structure: helices and β-sheets

6YGJ contains 26 α-helices and 0 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	21-33	13
α-helix	37-39	3
α-helix	40-70	31
α-helix	75-102	28
α-helix	103-107	5
α-helix	114-132	19
α-helix	137-161	25
α-helix	167-182	16
α-helix	187-202	16
α-helix	205-207	3
α-helix	210-230	21

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	120-134	15

Chain F: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	21-33	13
α-helix	40-68	29
α-helix	77-102	26
α-helix	103-107	5
α-helix	108-110	3
α-helix	114-132	19
α-helix	138-161	24
α-helix	167-182	16
α-helix	187-203	17
α-helix	210-212	3
α-helix	213-229	17

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	118-134	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
14-3-3 protein beta/alpha	A	protein	229	Homo sapiens	P31946 (AlphaFold model)
Carbohydrate-responsive element-binding protein	B, I	protein	21	Homo sapiens	Q9NP71 (AlphaFold model)
14-3-3 protein beta/alpha	F	protein	231	Homo sapiens	P31946 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YGJ_1 14-3-3 protein beta/alpha (chains A)
DKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRV
ISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKM
KGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEI
LNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTS

Sequence of entity 2 (B, I), FASTA

>6YGJ_2 Carbohydrate-responsive element-binding protein (chains B, I)
RDKIRLNNAIWRAWYIQYVQR

Sequence of entity 3 (F), FASTA

>6YGJ_3 14-3-3 protein beta/alpha (chains F)
TMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSW
RVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYL
KMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY
EILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTS

Ligands and cofactors

ID	Name	Formula	Copies
OQE	[2-[2-oxidanylidene-2-(2-phenylethylamino)ethoxy]phenyl]phosphonic acid	C16 H18 N O5 P	2

Primary citation

Structure-based evolution of a promiscuous inhibitor to a selective stabilizer of protein-protein interactions. Sijbesma, E., Visser, E., Plitzko, K. et al. Nat Commun (2020) 11:3954-3954. DOI 10.1038/s41467-020-17741-0 · PubMed

Other PDB entries of the same protein (UniProt P31946 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EQ8 1.5 Å, The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y130
5N10 1.6 Å, Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform
6HEP 1.86 Å, Crystal structure of human 14-3-3 beta in complex with CFTR R-domain peptide pS753-pS768
8EQH 1.9 Å, The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y213
6A5Q 2.0 Å, Structure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif
4DNK 2.2 Å, Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation…
6GN8 2.34 Å, Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta,…
2BQ0 2.5 Å, 14-3-3 Protein Beta (Human)
6GNK 2.55 Å, Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta,…
9GCP 2.59 Å, ChREBP/14-3-3 complex stabilized by AMP
2C23 2.65 Å, 14-3-3 Protein Beta (Human) in complex with exoenzyme S peptide
6BYK 3.0 Å, Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide

Browse structure collections

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