6M90: F-box/WD repeat-containing protein 1A

Name: PDB 6M90: Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
Published: 2019-04-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex. Determined by X-ray diffraction at 2.05 Å resolution. Released 3 Apr 2019.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,413
Mol. weight: 70.39 kDa
Ligands: PO4, J91
Released: 3 Apr 2019

Explore 6M90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M90 contains 18 α-helices and 31 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: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	144-150	7
α-helix	154-162	9
α-helix	166-173	8
α-helix	177-185	9
α-helix	188-199	12
α-helix	201-210	10
α-helix	212-215	4
α-helix	229-252	24
β-strand	256-261	6	1
β-strand	270-275	6	2
β-strand	279-284	6	2
β-strand	289-293	5	2
β-strand	299-303	5	2
β-strand	310-315	6	3
β-strand	319-324	6	3
β-strand	328-333	6	3
β-strand	339-344	6	3
β-strand	350-356	7	4
β-strand	359-364	6	4
β-strand	369-376	8	4
β-strand	379-386	8	4
β-strand	393-398	6	5
β-strand	402-407	6	5
β-strand	412-416	5	5
β-strand	422-426	5	5
β-strand	433-439	7	6
β-strand	442-447	6	6
β-strand	452-456	5	6
β-strand	462-466	5	6
β-strand	473-478	6	7
β-strand	482-487	6	7
β-strand	491-496	6	7
α-helix	497-500	4
α-helix	507-509	3
β-strand	511-516	6	7
β-strand	522-527	6	1
β-strand	531-536	6	1
β-strand	540-545	6	1

Chain B: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	13-17	5	8
α-helix	18-21	4
α-helix	25-32	8
β-strand	39-40	2	8
α-helix	46-58	13
α-helix	69-74	6
α-helix	79-92	14
α-helix	95-109	15
α-helix	114-121	8
α-helix	129-137	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
F-box/WD repeat-containing protein 1A	A	protein	432	Homo sapiens	Q9Y297 (AlphaFold model)
Skp1	B	protein	144	Homo sapiens	P63208 (AlphaFold model)
Catenin beta-1	C	protein	33	Homo sapiens	P35222 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6M90_1 F-box/WD repeat-containing protein 1A (chains A)
SMLQRDFITALPARGLDHIAENILSYLDAKSLCAAELVCKEWYRVTSDGMLWKKLIERMV
RTDSLWRGLAERRGWGQYLFKNKPPDGNAPPNSFYRALYPKIIQDIETIESNWRCGRHSL
QRIHCRSETSKGVYCLQYDDQKIVSGLRDNTIKIWDKNTLECKRILTGHTGSVLCLQYDE
RVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASP
TDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQ
YRDRLVVSGSSDNTIRLWDIECGACLRVLEGHEELVRCIRFDNKRIVSGAYDGKIKVWDL
VAALDPRAPAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTILIWDFLNDPAAQAEPP
RSPSRTYTYISR

Sequence of entity 2 (B), FASTA

>6M90_2 Skp1 (chains B)
PSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHKD
DPPDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTF
NIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 3 (C), FASTA

>6M90_3 Catenin beta-1 (chains C)
CDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
J91	2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbony…	C20 H12 F4 N2 O5	2

Primary citation

Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction. Simonetta, K.R., Taygerly, J., Boyle, K. et al. Nat Commun (2019) 10:1402-1402. DOI 10.1038/s41467-019-09358-9 · PubMed

Other PDB entries of the same protein (UniProt Q9Y297 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T9W 1.16 Å, Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide
9TES 1.22 Å, Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
9TDZ 1.35 Å, Crystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide
9TG7 1.68 Å, Crystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide
9T8Y 1.79 Å, Crystal structure of beta-TrCP bound by monophosphorylated NRF2 degron peptide.
9TFU 2.0 Å, Crystal structure of beta-TrCP bound by monophosphorylated ATF4 degron peptide
9T95 2.15 Å, Crystal structure of beta-TrCP bound by diphosphorylated NRF2 degron peptide.
6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
2P64 2.5 Å, D domain of b-TrCP
6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
6M94 2.7 Å, Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex

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