5VZU: Skp1-FBXO31-cyclin D1 complex

Crystal structure of the Skp1-FBXO31-cyclin D1 complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,361
Mol. weight: 150.14 kDa
Ligands: PO4, ZN
Released: 17 Jan 2018

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

Secondary structure: helices and β-sheets

5VZU contains 65 α-helices and 55 β-strands across 6 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: 9 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	1113-1127	15
α-helix	1132-1139	8
α-helix	1147-1156	10
α-helix	1158-1161	4

Chain B: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	67-69	3
α-helix	72-80	9
α-helix	87-91	5
α-helix	95-100	6
α-helix	104-115	12
α-helix	121-127	7
α-helix	131-134	4
α-helix	135-139	5
α-helix	143-145	3
β-strand	147-151	5	2
β-strand	157	1	3
β-strand	160-165	6	2
β-strand	168-175	8	2
α-helix	185-186	2
β-strand	187-195	9	2
α-helix	201-202	2
β-strand	203-206	4	2
β-strand	214-222	9	2
β-strand	225-230	6	2
α-helix	233-236	4
α-helix	242-254	13
α-helix	258-261	4
α-helix	265-278	14
β-strand	284-289	6	2
β-strand	291	1	4
α-helix	292-294	3
β-strand	303-308	6	5
α-helix	310-312	3
β-strand	314-321	8	5
β-strand	325-330	6	5
β-strand	332	1	3
β-strand	342-352	11	5
α-helix	357-361	5
α-helix	363-382	20
β-strand	444-445	2	6
α-helix	448-449	2
β-strand	453-454	2	5
β-strand	462-463	2	6
β-strand	465-475	11	5
β-strand	479-492	14	5
β-strand	495-500	6	5
α-helix	501-503	3
β-strand	505-511	7	5
β-strand	520	1	4
α-helix	524-537	14

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1003-1007	5	7
β-strand	1014-1017	4	7
α-helix	1018-1021	4
α-helix	1025-1032	8
β-strand	1045-1046	2	7
α-helix	1052-1064	13
α-helix	1087-1093	7
α-helix	1097-1110	14
α-helix	1113-1127	15
α-helix	1132-1138	7
α-helix	1147-1156	10
α-helix	1158-1161	4

Chain D: 22 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	67-69	3
α-helix	72-80	9
α-helix	84-86	3
α-helix	87-91	5
α-helix	95-100	6
α-helix	104-115	12
α-helix	121-127	7
α-helix	131-133	3
α-helix	134-139	6
α-helix	140-142	3
α-helix	143-145	3
β-strand	147-151	5	8
β-strand	153	1	9
β-strand	155	1	9
β-strand	157	1	10
β-strand	159-165	7	8
β-strand	168-175	8	8
α-helix	185-186	2
β-strand	187-197	11	8
β-strand	200-206	7	8
β-strand	214-215	2	8
β-strand	217-222	6	8
β-strand	225-229	5	8
α-helix	233-236	4
α-helix	241-254	14
α-helix	264-278	15
β-strand	284-289	6	8
β-strand	291	1	11
α-helix	292-294	3
β-strand	303-308	6	12
α-helix	310-312	3
β-strand	314-321	8	12
β-strand	325-330	6	12
β-strand	332	1	10
β-strand	344-351	8	12
α-helix	353-355	3
α-helix	357-360	4
α-helix	363-382	20
β-strand	444-445	2	13
α-helix	448-449	2
β-strand	453	1	12
β-strand	462-463	2	13
β-strand	465-475	11	12
β-strand	479-492	14	12
β-strand	495-500	6	12
β-strand	505-511	7	12
β-strand	520	1	11
α-helix	524-537	14

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	288-290	3
α-helix	292-294	3

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	292-294	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1	A, C	protein	149	Homo sapiens	P63208 (AlphaFold model)
F-box only protein 31	B, D	protein	488	Homo sapiens	Q5XUX0 (AlphaFold model)
Cyclin D1	E, F	protein	17	Homo sapiens	P24385 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5VZU_1 S-phase kinase-associated protein 1 (chains A, C)
MASIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHK
DDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEE
IRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (B, D), FASTA

>5VZU_2 F-box only protein 31 (chains B, D)
MASWSHPQFEKSGRSLLELPPELLVEIFASLPGTDLPSLAQVCTKFRRILHTDTIWRRRC
REEYGVCENLRKLEITGVSCRDVYAKLLHRYRHILGLWQPDIGPYGGLLNVVVDGLFIIG
WMYLPPHDPHVDDPMRFKPLFRIHLMERKAATVECMYGHKGPHHGHIQIVKKDEFSTKCN
QTDHHRMSGGRQEEFRTWLREEWGRTLEDIFHEHMQELILMKFIYTSQYDNCLTYRRIYL
PPSRPDDLIKPGLFKGTYGSHGLEIVMLSFHGRRARGTKITGDPNIPAGQQTVEIDLRHR
IQLPDLENQRNFNELSRIVLEVRERVRQEQQEGGHEAGEGRGRQGPRESQPSPAQPRAEA
PSKGPDGTPGEDGGEPGDAVAAAEQPAQCGQGQPFVLPVGVSSRNEDYPRTCRMCFYGTG
LIAGHGFTSPERTPGVFILFDEDRFGFVWLELKSFSLYSRVQATFRNADAPSPQAFDEML
KNIQSLTS

Sequence of entity 3 (E, F), FASTA

>5VZU_3 Cyclin D1 (chains E, F)
EEVDLACTPTDVRDVDI

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	10
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCFFBXO31 ubiquitin ligase. Li, Y., Jin, K., Bunker, E. et al. Proc Natl Acad Sci U S A (2018) 115:319-324. DOI 10.1073/pnas.1708677115 · 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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