8GRE: F-box protein

F-box protein in complex with skp1(FL) and substrate. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 10,749
Mol. weight: 168.51 kDa
Released: 26 Apr 2023

Explore 8GRE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GRE contains 81 α-helices and 32 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: 27 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	26-48	23
β-strand	52-57	6	1
α-helix	58-61	4
β-strand	69-72	4	2
β-strand	76-79	4	3
β-strand	83-86	4	3
β-strand	89	1	3
α-helix	91-97	7
β-strand	100	1	4
β-strand	107	1	4
α-helix	108	1
α-helix	109-118	10
α-helix	121-123	3
α-helix	124-136	13
α-helix	139-141	3
α-helix	142-150	9
α-helix	157-167	11
α-helix	168-171	4
α-helix	173-180	8
α-helix	184-186	3
α-helix	187-214	28
α-helix	228-236	9
α-helix	241-253	13
α-helix	262-272	11
α-helix	277-288	12
α-helix	296-311	16
α-helix	317-329	13
β-strand	337-339	3	5
α-helix	347-359	13
α-helix	364-383	20
β-strand	388-391	4	5
α-helix	394-403	10
α-helix	409-411	3
α-helix	412-433	22
α-helix	436-438	3
β-strand	442-444	3	6
α-helix	446-458	13

Chain B: 29 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
α-helix	26-48	23
β-strand	52-57	6	1
α-helix	58-61	4
β-strand	69-72	4	6
β-strand	76-79	4	7
β-strand	83-86	4	7
β-strand	89	1	7
α-helix	91-97	7
β-strand	100	1	8
β-strand	107	1	8
α-helix	108	1
α-helix	109-118	10
α-helix	121-123	3
α-helix	124-136	13
α-helix	139-141	3
α-helix	142-150	9
α-helix	157-167	11
α-helix	168-171	4
α-helix	173-179	7
α-helix	184-186	3
α-helix	187-214	28
α-helix	228-236	9
α-helix	241-253	13
α-helix	262-272	11
α-helix	277-288	12
α-helix	296-311	16
α-helix	317-329	13
β-strand	337-339	3	9
α-helix	347-359	13
α-helix	364-383	20
β-strand	388-391	4	9
α-helix	393-395	3
α-helix	397-403	7
α-helix	409-411	3
α-helix	412-433	22
α-helix	436-438	3
β-strand	442-444	3	2
α-helix	446-458	13

Chain C: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	13-22	10
α-helix	24-27	4
α-helix	32-49	18
α-helix	55-69	15
α-helix	72-79	8
β-strand	86	1	10
α-helix	94-96	3
β-strand	97	1	10
α-helix	104-112	9
α-helix	114-116	3
β-strand	117-118	2	11
β-strand	147-157	11	12
β-strand	170-177	8	11
α-helix	182-188	7
β-strand	189-195	7	12
β-strand	202-204	3	12
α-helix	210-213	4
β-strand	218-226	9	11
α-helix	227-229	3
α-helix	233-236	4
β-strand	243-252	10	12
β-strand	264-270	7	11
β-strand	280-285	6	11
α-helix	291-293	3
α-helix	297-314	18
α-helix	318-319	2
β-strand	341-344	4	11
α-helix	353-358	6
α-helix	360-361	2

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	86-95	10
α-helix	114-117	4
α-helix	118-123	6
α-helix	128-140	13
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-190	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Citrate synthase	A, B	protein	460	Saccharomyces cerevisiae	P08679 (AlphaFold model)
F-box protein UCC1	C	protein	369	Saccharomyces cerevisiae	Q05947 (AlphaFold model)
E3 ubiquitin ligase complex SCF subunit	D	protein	194	Saccharomyces cerevisiae	P52286 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8GRE_1 Citrate synthase (chains A, B)
MTVPYLNSNRNVASYLQSNSSQEKTLKERFSEIYPIHAQDVRQFVKEHGKTKISDVLLEQ
VYGGMRGIPGSVWEGSVLDPEDGIRFRGRTIADIQKDLPKAKGSSQPLPEALFWLLLTGE
VPTQAQVENLSADLMSRSELPSHVVQLLDNLPKDLHPMAQFSIAVTALESESKFAKAYAQ
GISKQDYWSYTFEDSLDLLGKLPVIAAKIYRNVFKDGKMGEVDPNADYAKNLVNLIGSKD
EDFVDLMRLYLTIHSDHEGGNVSAHTSHLVGSALSSPYLSLASGLNGLAGPLHGRANQEV
LEWLFALKEEVNDDYSKDTIEKYLWDTLNSGRVIPGYGHAVLRKTDPRYMAQRKFAMDHF
PDYELFKLVSSIYEVAPGVLTEHGKTKNPWPNVDAHSGVLLQYYGLKESSFYTVLFGVSR
AFGILAQLITDRAIGASIERPKSYSTEKYKELVKNIESKL

Sequence of entity 2 (C), FASTA

>8GRE_2 F-box protein UCC1 (chains C)
MNQSDSSLMDLPLEIHLSLLEYVPNELRAVNKYFYVLHNHSYKEKSLAWIAEDNYIWAVV
KHSLCLYVKSLDPLRQHAREIIQETKEPGFNVPLCMTKYIADSWYIVYNALQYPGKIINM
GWDKYTKSQDLNGSDSTSNFNSRPKERTLMQSLTALPVNFWSRKKDEPTPVNVWFYVKNA
HVARYIPKIITEIGICNYGPKQIVASAGYINELITSEGIYCVNLGHLPRLYDEQIFEGTG
TTHLPLELKAIDRTDSDVCINSDLVLLGYDFIPYQISKPWLLFRIEPVNSIEAIFNYSEC
SFSYQFAWSLACLQSEEKISFPRDTIIGHGLPYKPSKLIRIFVYKHPEQKQDLGQEIALP
NWNTPYLRR

Sequence of entity 3 (D), FASTA

>8GRE_3 E3 ubiquitin ligase complex SCF subunit (chains D)
MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSK
DNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWD
REFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEE
EAAIRRENEWAEDR

Primary citation

Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Nishio, K., Kawarasaki, T., Sugiura, Y. et al. Sci Adv (2023) 9:eadf1956-eadf1956. DOI 10.1126/sciadv.adf1956 · PubMed

Other PDB entries of the same protein (UniProt P08679 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GR9 1.48 Å, Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae…
8GR8 2.39 Å, Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomycescerevisiae
8GRF 2.53 Å, Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL)…

Browse structure collections

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