8GRF: Citrate synthase

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate. Determined by X-ray diffraction at 2.53 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 2.53 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 11,186
Mol. weight: 168.76 kDa
Released: 26 Apr 2023

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

Secondary structure: helices and β-sheets

8GRF contains 83 α-helices and 35 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	109-118	10
α-helix	124-136	13
α-helix	139-141	3
α-helix	142-148	7
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	218-221	4
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	1	5
α-helix	347-359	13
α-helix	364-383	20
β-strand	391	1	5
α-helix	393-395	3
α-helix	397-403	7
α-helix	409-411	3
α-helix	412-434	23
α-helix	436-438	3
β-strand	442-444	3	6
α-helix	446-459	14

Chain B: 28 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	296-310	15
α-helix	317-330	14
β-strand	337	1	9
α-helix	347-359	13
α-helix	364-383	20
β-strand	391	1	9
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	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	55-70	16
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	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	349-351	3
α-helix	353-358	6
α-helix	360-361	2

Chain D: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	13
β-strand	15-19	5	13
α-helix	20-23	4
α-helix	27-30	4
β-strand	77-79	3	13
α-helix	84-96	13
α-helix	108-113	6
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

>8GRF_1 Citrate synthase (chains A, B)
MTVPYLNSNRNVASYLQSNSSQEKTLKERFSEIYPIHAQDVRQFVKEHGKTKISDVLLEQ
VYGGMRGIPGSVWEGSVLDPEDGIRFRGRTIADIQKDLPKAKGSSQPLPEALFWLLLTGE
VPTQAQVENLSADLMSRSELPSHVVQLLDNLPKDLHPMAQFSIAVTALESESKFAKAYAQ
GISKQDYWSYTFEDSLDLLGKLPVIAAKIYRNVFKDGKMGEVDPNADYAKNLVNLIGSKD
EDFVDLMRLYLTIHSDHEGGNVSAHTSHLVGSALSSPYLSLASGLNGLAGPLHGRANQEV
LEWLFALKEEVNDDYSKDTIEKYLWDTLNSGRVIPGYGHAVLRKTDPRYMAQRKFAMDHF
PDYELFKLVSSIYEVAPGVLTEHGKTKNPWPNVDAHSGVLLQYYGLKESSFYTVLFGVSR
AFGILAQLITDRAIGASIERPKSYSTEKYKELVKNIESKL

Sequence of entity 2 (C), FASTA

>8GRF_2 F-box protein UCC1 (chains C)
MNQSDSSLMDLPLEIHLSLLEYVPNELRAVNKYFYVLHNHSYKEKSLAWIAEDNYIWAVV
KHSLCLYVKSLDPLRQHAREIIQETKEPGFNVPLCMTKYIADSWYIVYNALQYPGKIINM
GWDKYTKSQDLNGSDSTSNFNSRPKERTLMQSLTALPVNFWSRKKDEPTPVNVWFYVKNA
HVARYIPKIITEIGICNYGPKQIVASAGYINELITSEGIYCVNLGHLPRLYDEQIFEGTG
TTHLPLELKAIDRTDSDVCINSDLVLLGYDFIPYQISKPWLLFRIEPVNSIEAIFNYSEC
SFSYQFAWSLACLQSEEKISFPRDTIIGHGLPYKPSKLIRIFVYKHPEQKQDLGQEIALP
NWNTPYLRR

Sequence of entity 3 (D), FASTA

>8GRF_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…
8GRE 2.3 Å, F-box protein in complex with skp1(FL) and substrate
8GR8 2.39 Å, Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomycescerevisiae

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