6X90: Guanine nucleotide exchange factor Sec12

Structure of the guanine nucleotide exchange factor Sec12 bound to the small GTPase Sar1. Determined by X-ray diffraction at 2.26 Å resolution. Released 24 Mar 2021.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 3,826
Mol. weight: 59.01 kDa
Released: 24 Mar 2021

Explore 6X90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X90 contains 12 α-helices and 33 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	8
α-helix	36-45	10
β-strand	70-72	3	8
α-helix	77-86	10
β-strand	93-99	7	8
α-helix	103-105	3
α-helix	106-117	12
α-helix	120-122	3
β-strand	127-132	6	8
α-helix	142-149	8
β-strand	166-170	5	8
α-helix	179-192	14

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	14-19	6	2
β-strand	24-30	7	2
β-strand	40-47	8	2
α-helix	54-57	4
β-strand	58-65	8	2
α-helix	66-67	2
α-helix	71-73	3
β-strand	75-79	5	3
β-strand	82-86	5	3
α-helix	91-95	5
β-strand	103-108	6	3
β-strand	115-121	7	3
β-strand	133-138	6	4
β-strand	145-149	5	4
β-strand	155-160	6	4
β-strand	165-171	7	4
β-strand	178-181	4	5
β-strand	187-191	5	5
β-strand	196-200	5	5
β-strand	206-210	5	5
β-strand	217-226	10	6
β-strand	229-236	8	6
β-strand	242-249	8	6
β-strand	254-263	10	6
β-strand	269-274	6	7
β-strand	280-285	6	7
β-strand	290-294	5	7
β-strand	299-304	6	7
β-strand	312-317	6	1
β-strand	323-328	6	1
β-strand	332-337	6	1
α-helix	338-339	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-exchange factor SEC12	B	protein	360	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P11655 (AlphaFold model)
Small COPII coat GTPase SAR1	A	protein	173	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20606 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6X90_1 Guanine nucleotide-exchange factor SEC12 (chains B)
MKFVTASYNVGYPAYGAKFLNNDTLLVAGGGGEGNNGIPNKLTVLRVDPTKDTEKEQFHI
LSEFALEDNDDSPTAIDASKGIILVGCNENSTKITQGKGNKHLRKFKYDKVNDQLEFLTS
VDFDASTNADDYTKLVYISREGTVAAIASSKVPAIMRIIDPSDLTEKFEIETRGEVKDLH
FSTDGKVVAYITGSSLEVISTVTGSCIARKTDFDKNWSLSKINFIADDTVLIAASLKKGK
GIVLTKISIKSGNTSVLRSKQVTNRFKGITSMDVDMKGELAVLASNDNSIALVKLKDLSM
SKIFKQAHSFAITEVTISPDSTYVASVSAANTIHIIKLPLNYANYTSMKQKISKHHHHHH

Sequence of entity 2 (A), FASTA

>6X90_2 Small COPII coat GTPase SAR1 (chains A)
GKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRL
WKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNAVSEA
ELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQYIHHHHHH

Primary citation

Structural basis for the initiation of COPII vesicle biogenesis. Joiner, A.M.N., Fromme, J.C. Structure (2021) 29:859-872.e6. DOI 10.1016/j.str.2021.03.013 · PubMed

Other PDB entries of the same protein (UniProt P11655 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4H5I 1.36 Å, Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)
4H5J 2.6 Å, Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P64 form)

Browse structure collections

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