1XB4: PDB entry 1XB4

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II. Determined by X-ray diffraction at 3.1 Å resolution. Released 22 Mar 2005.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 5,773
Mol. weight: 94.33 kDa
Released: 22 Mar 2005

Explore 1XB4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XB4 contains 30 α-helices and 40 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: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-13	3
α-helix	16-17	2
α-helix	20-40	21
β-strand	45-47	3	1
β-strand	51	1	2
β-strand	52	1	1
α-helix	53	1
β-strand	74	1	2
β-strand	77-78	2	3
β-strand	83-84	2	3
α-helix	87-99	13
β-strand	103-106	4	1
β-strand	111	1	1
β-strand	120-123	4	1
α-helix	128-140	13
β-strand	149-150	2	4
α-helix	151-154	4
α-helix	170-181	12
α-helix	182-184	3
β-strand	187-190	4	4
β-strand	196-200	5	4

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	11-13	3
α-helix	20-40	21
β-strand	45-47	3	5
β-strand	77-78	2	6
β-strand	83-84	2	6
α-helix	87-99	13
β-strand	103-106	4	5
β-strand	111	1	5
β-strand	120-123	4	5
α-helix	128-140	13
β-strand	149-150	2	7
α-helix	151-155	5
α-helix	170-181	12
α-helix	182-184	3
β-strand	187-190	4	7
β-strand	196-200	5	7

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	11-13	3
α-helix	20-40	21
β-strand	45-47	3	8
β-strand	51	1	9
β-strand	52-53	2	8
β-strand	74	1	9
β-strand	77-78	2	10
β-strand	83-84	2	10
α-helix	87-99	13
β-strand	103-106	4	8
β-strand	120-123	4	8
α-helix	128-140	13
β-strand	148-150	3	11
α-helix	170-181	12
α-helix	182-184	3
β-strand	187-190	4	11
β-strand	196-200	5	11

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	26-40	15
β-strand	77-78	2	12
β-strand	83-84	2	12
α-helix	87-99	13
β-strand	103-104	2	13
β-strand	122-123	2	13
α-helix	128-138	11
β-strand	148-150	3	14
α-helix	173-182	10
β-strand	190	1	15
β-strand	196	1	15
β-strand	198-200	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region	A, B, C, D	protein	202	Saccharomyces cerevisiae	P47142 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1XB4_1 Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region (chains A, B, C, D)
MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDS
GSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTR
YFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPL
CDRNRATMLKDENDKVIAIKVV

Primary citation

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II. Wernimont, A.K., Weissenhorn, W. BMC Struct Biol (2004) 4:10-10. DOI 10.1186/1472-6807-4-10 · PubMed

Other PDB entries of the same protein (UniProt P47142 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U5T 3.6 Å, Structure of the ESCRT-II endosomal trafficking complex
1W7P 3.6 Å, The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36)

Browse structure collections

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