2F6M: Vps23-C:Vps28-N subcomplex

Structure of a Vps23-C:Vps28-N subcomplex. Determined by X-ray diffraction at 2.1 Å resolution. Released 18 Apr 2006.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 2,913
Mol. weight: 41.8 kDa
Ligands: MG, DDQ
Released: 18 Apr 2006

Explore 2F6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2F6M contains 14 α-helices and 0 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	323-351	29
α-helix	356-381	26

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	14-17	4
α-helix	31-58	28
α-helix	64-82	19
α-helix	89-103	15
α-helix	109-117	9

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	323-351	29
α-helix	356-380	25

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	31-58	28
α-helix	64-82	19
α-helix	87-93	7
α-helix	99-103	5
α-helix	109-116	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease	A, C	protein	65	Saccharomyces cerevisiae	P25604 (AlphaFold model)
Vacuolar protein sorting-associated protein VPS28	B, D	protein	109	Saccharomyces cerevisiae	Q02767 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2F6M_1 Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease (chains A, C)
MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRI
TSPLS

Sequence of entity 2 (B, D), FASTA

>2F6M_2 Vacuolar protein sorting-associated protein VPS28 (chains B, D)
GAMDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTN
TVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
DDQ	Decylamine-n,n-dimethyl-N-oxide	C12 H27 N O	8

Primary citation

Structural and functional organization of the ESCRT-I trafficking complex. Kostelansky, M.S., Sun, J., Lee, S. et al. Cell (2006) 125:113-126. DOI 10.1016/j.cell.2006.01.049 · PubMed

Other PDB entries of the same protein (UniProt P25604 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3R3Q 1.45 Å, Crystal structure of the yeast Vps23 UEV domain
1UZX 1.85 Å, A complex of the Vps23 UEV with ubiquitin
3R42 1.87 Å, Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
2P22 2.7 Å, Structure of the Yeast ESCRT-I Heterotetramer Core
2F66 2.8 Å, Structure of the ESCRT-I endosomal trafficking complex
2CAZ 3.6 Å, ESCRT-I core

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