2J9U: Vacuolar protein sorting-associated protein 28

2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Jan 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 4
Atoms: 2,295
Mol. weight: 39.07 kDa
Ligands: ZN
Released: 23 Jan 2007

Explore 2J9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2J9U contains 18 α-helices and 14 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.

Chains A and C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	150-168	19
β-strand	173	1	1
α-helix	174-191	18
α-helix	199-210	12
β-strand	217	1	1
α-helix	220-240	21

Chains B and D: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	116-119	4	2
β-strand	126-129	4	2
α-helix	140-141	2
β-strand	142	1	3
α-helix	148	1
β-strand	149	1	3
α-helix	150-151	2
α-helix	152-155	4
α-helix	156-158	3
β-strand	160	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 28	A, C	protein	96	SACCHAROMYCES CEREVISIAE	Q02767 (AlphaFold model)
Vacuolar protein sorting-associated protein 36	B, D	protein	76	SACCHAROMYCES CEREVISIAE	Q06696 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2J9U_1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 (chains A, C)
MFNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWI
VRINKLSIGDTLTETQIRELLFDLELAYKSFYALLD

Sequence of entity 2 (B, D), FASTA

>2J9U_2 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36 (chains B, D)
MAHHHHHHMASADVVSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSIN
CSNAIDPNANPRNQFG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural Insight Into the Escrt-I/-II Link and its Role in Mvb Trafficking. Gill, D.J., Teo, H.L., Sun, J. et al. EMBO J (2007) 26:600. DOI 10.1038/SJ.EMBOJ.7601501 · PubMed

Other PDB entries of the same protein (UniProt Q02767 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J9V 2.0 Å, 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus
2F6M 2.1 Å, Structure of a Vps23-C:Vps28-N subcomplex
2P22 2.7 Å, Structure of the Yeast ESCRT-I Heterotetramer Core
2F66 2.8 Å, Structure of the ESCRT-I endosomal trafficking complex
2G3K 3.05 Å, Crystal structure of the C-terminal domain of Vps28
2CAZ 3.6 Å, ESCRT-I core

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