7T1Z: Fbw7-Skp1-MycNdegron complex

Structure of the Fbw7-Skp1-MycNdegron complex. Determined by X-ray diffraction at 2.77 Å resolution. Released 16 Feb 2022.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,701
Mol. weight: 71.41 kDa
Released: 16 Feb 2022

Explore 7T1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T1Z contains 17 α-helices and 35 β-strands across 3 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	13-16	4	1
α-helix	18-21	4
α-helix	25-32	8
β-strand	45-46	2	1
α-helix	52-64	13
α-helix	99-109	11
α-helix	113-125	13
α-helix	132-138	7
α-helix	147-156	10

Chain B: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	265-269	5
α-helix	274-276	3
α-helix	286-293	8
α-helix	298-304	7
α-helix	309-314	6
α-helix	318-327	10
α-helix	350-367	18
α-helix	371-373	3
β-strand	374-377	4	2
β-strand	384-390	7	3
β-strand	393-398	6	3
β-strand	403-407	5	3
β-strand	413-417	5	3
β-strand	424-429	6	4
β-strand	433-438	6	4
β-strand	443-447	5	4
β-strand	453-457	5	4
β-strand	464-470	7	5
β-strand	473-478	6	5
β-strand	483-487	5	5
β-strand	493-497	5	5
β-strand	504-509	6	6
β-strand	514-518	5	6
β-strand	522-527	6	6
β-strand	532-538	7	6
β-strand	544-549	6	7
β-strand	553-558	6	7
β-strand	563-567	5	7
β-strand	573-577	5	7
β-strand	584-590	7	8
β-strand	593-598	6	8
β-strand	602-607	6	8
β-strand	612-617	6	8
β-strand	627-632	6	9
β-strand	636-641	6	9
β-strand	645-650	6	9
β-strand	656-662	7	9
α-helix	666-668	3
β-strand	671-677	7	2
β-strand	681-687	7	2
β-strand	696-701	6	2

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	59-61	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1	A	protein	149	Homo sapiens	P63208 (AlphaFold model)
F-box/WD repeat-containing protein 7	B	protein	457	Homo sapiens	Q969H0 (AlphaFold model)
Myc proto-oncogene N terminal degron	C	protein	20	Homo sapiens	P01106 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7T1Z_1 S-phase kinase-associated protein 1 (chains A)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPGGSGTDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEE
IRKTFNIKNDFTEEEEAQVRKENQWTEEE

Sequence of entity 2 (B), FASTA

>7T1Z_2 F-box/WD repeat-containing protein 7 (chains B)
SHHHHHHGGSGMTQVKHMMQVIEPQFQRDFISLLPKELALYVLSFLEPKDLLQAAQTCRY
WRILAEDNLLWREKCKEEGIDEPLHIKRRKVIKPGFIHSPWKSAYIRQHRIDTNWRRGEL
KSPKVLKGHDDHVITCLQFCGNRIVSGSDDNTLKVWSAVTGKCLRTLVGHTGGVWSSQMR
DNIIISGSTDRTLKVWNAETGECIHTLYGHTSTVRCMHLHEKRVVSGSRDATLRVWDIET
GQCLHVLMGHVAAVRCVQYDGRRVVSGAYDFMVKVWDPETETCLHTLQGHTNRVYSLQFD
GIHVVSGSLDTSIRVWDVETGNCIHTLTGHQSLTSGMELKDNILVSGNADSTVKIWDIKT
GQCLQTLQGPNKHQSAVTCLQFNKNFVITSSDDGTVKLWDLKTGEFIRNLVTLESGGSGG
VVWRIRASNTKLVCAVGSRNGTEETKLLVLDFDVDMK

Sequence of entity 3 (C), FASTA

>7T1Z_3 Myc proto-oncogene N terminal degron (chains C)
EDIWKKFELLPTPPLSPSRR

Primary citation

Two diphosphorylated degrons control c-Myc degradation by the Fbw7 tumor suppressor. Welcker, M., Wang, B., Rusnac, D.V. et al. Sci Adv (2022) 8:eabl7872-eabl7872. DOI 10.1126/sciadv.abl7872 · PubMed

Other PDB entries of the same protein (UniProt P63208 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FS1 1.8 Å, Insights into scf ubiquitin ligases from the structure of the SKP1-SKP2 complex
6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
2AST 2.3 Å, Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
2E31 2.4 Å, Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
2OVR 2.5 Å, Structure of the Skp1-Fbw7-CyclinEdegN complex
6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
6WNX 2.5 Å, FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
5IBK 2.5 Å, Skp1-F-box in complex with a ubiquitin variant
6O60 2.5 Å, Crystal structure of GGTase3-FBXL2-SKP1 complex
5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

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