8GR9: Citrate synthase

Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A. Determined by X-ray diffraction at 1.48 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.48 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 7,825
Mol. weight: 104.35 kDa
Ligands: COA, OAA
Released: 26 Apr 2023

Explore 8GR9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GR9 contains 56 α-helices and 20 β-strands across 2 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: 29 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	221-223	3
α-helix	228-236	9
α-helix	241-253	13
α-helix	262-272	11
α-helix	277-288	12
α-helix	296-309	14
α-helix	317-329	13
β-strand	337	1	5
α-helix	347-359	13
α-helix	364-373	10
α-helix	376-383	8
β-strand	391	1	5
α-helix	394-403	10
α-helix	409-411	3
α-helix	412-434	23
α-helix	436-439	4
β-strand	442-444	3	6
α-helix	446-458	13

Chain B: 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	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	317-329	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	394-403	10
α-helix	409-411	3
α-helix	412-433	22
α-helix	436-439	4
β-strand	442-444	3	2
α-helix	446-458	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Citrate synthase	A, B	protein	460	Saccharomyces cerevisiae	P08679 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8GR9_1 Citrate synthase (chains A, B)
MTVPYLNSNRNVASYLQSNSSQEKTLKERFSEIYPIHAQDVRQFVKEHGKTKISDVLLEQ
VYGGMRGIPGSVWEGSVLDPEDGIRFRGRTIADIQKDLPKAKGSSQPLPEALFWLLLTGE
VPTQAQVENLSADLMSRSELPSHVVQLLDNLPKDLHPMAQFSIAVTALESESKFAKAYAQ
GISKQDYWSYTFEDSLDLLGKLPVIAAKIYRNVFKDGKMGEVDPNADYAKNLVNLIGSKD
EDFVDLMRLYLTIHSDHEGGNVSAHTSHLVGSALSSPYLSLASGLNGLAGPLHGRANQEV
LEWLFALKEEVNDDYSKDTIEKYLWDTLNSGRVIPGYGHAVLRKTDPRYMAQRKFAMDHF
PDYELFKLVSSIYEVAPGVLTEHGKTKNPWPNVDAHSGVLLQYYGLKESSFYTVLFGVSR
AFGILAQLITDRAIGASIERPKSYSTEKYKELVKNIESKL

Ligands and cofactors

ID	Name	Formula	Copies
COA	Coenzyme a	C21 H36 N7 O16 P3 S	1
OAA	Oxaloacetate ion	C4 H3 O5	1

Water and common crystallization additives (GOL, K, CL) are not listed.

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:

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
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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