5V4B: Skp1-FBXW7-DISC1 complex

Crystal structure of the Skp1-FBXW7-DISC1 complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,910
Mol. weight: 69.61 kDa
Released: 20 Sept 2017

Explore 5V4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V4B contains 18 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: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1003-1007	5	1
β-strand	1013-1017	5	1
α-helix	1018-1021	4
α-helix	1025-1032	8
β-strand	1045-1046	2	1
α-helix	1052-1064	13
α-helix	1087-1092	6
α-helix	1097-1110	14
α-helix	1113-1125	13
α-helix	1132-1139	8
α-helix	1147-1156	10

Chain B: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	2264-2272	9
α-helix	2280-2283	4
α-helix	2286-2294	9
α-helix	2298-2304	7
α-helix	2309-2315	7
α-helix	2318-2327	10
α-helix	2350-2367	18
α-helix	2371-2373	3
β-strand	2374-2377	4	2
β-strand	2384-2390	7	3
β-strand	2393-2398	6	3
β-strand	2403-2407	5	3
β-strand	2413-2417	5	3
β-strand	2424-2430	7	4
β-strand	2433-2438	6	4
β-strand	2443-2447	5	4
β-strand	2453-2457	5	4
β-strand	2464-2470	7	5
β-strand	2473-2478	6	5
β-strand	2483-2487	5	5
β-strand	2493-2497	5	5
β-strand	2504-2509	6	6
β-strand	2514-2518	5	6
β-strand	2523-2527	5	6
α-helix	2528-2530	3
β-strand	2532-2537	6	6
β-strand	2544-2549	6	7
β-strand	2553-2558	6	7
β-strand	2563-2567	5	7
β-strand	2573-2577	5	7
β-strand	2584-2590	7	8
β-strand	2593-2598	6	8
β-strand	2603-2607	5	8
β-strand	2613-2617	5	8
β-strand	2627-2632	6	9
β-strand	2636-2641	6	9
β-strand	2645-2650	6	9
β-strand	2655-2662	8	9
β-strand	2670-2677	8	2
β-strand	2681-2688	8	2
β-strand	2696-2701	6	2

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	194-197	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1,S-phase kinase-associated protein 1	A	protein	149	Homo sapiens	P63208 (AlphaFold model)
F-box/WD repeat-containing protein 7	B	protein	444	Homo sapiens	Q969H0 (AlphaFold model)
DISC1 peptide	C	protein	15	Homo sapiens	Q9NRI5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V4B_1 S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 (chains A)
MASIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHK
DDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKAKTPEE
IRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (B), FASTA

>5V4B_2 F-box/WD repeat-containing protein 7 (chains B)
TQVKHMMQVIEPQFQRDFISLLPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLLWR
EKCKEEGIDEPLHIKRRKVIKPGFIHSPWKSAYIRQHRIDTNWRRGELKSPKVLKGHDDH
VITCLQFCGNRIVSGSDDNTLKVWSAVTGKCLRTLVGHTGGVWSSQMRDNIIISGSTDRT
LKVWNAETGECIHTLYGHTSTVRCMHLHEKRVVSGSRDATLRVWDIETGQCLHVLMGHVA
AVRCVQYDGRRVVSGAYDFMVKVWDPETETCLHTLQGHTNRVYSLQFDGIHVVSGSLDTS
IRVWDVETGNCIHTLTGHQSLTSGMELKDNILVSGNADSTVKIWDIKTGQCLQTLQGPNK
HQSAVTCLQFNKNFVITSSDDGTVKLWDLKTGEFIRNLVTLESGGSGGVVWRIRASNTKL
VCAVGSRNGTEETKLLVLDFDVDM

Sequence of entity 3 (C), FASTA

>5V4B_3 DISC1 peptide (chains C)
PEVPPTPPGSHSAFT

Primary citation

FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system. Yalla, K., Elliott, C., Day, J.P. et al. Mol Psychiatry (2018) 23:1278-1286. DOI 10.1038/mp.2017.138 · 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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