2J9U
2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d2j9ua_ | All alpha proteins | Four-helical up-and-down bundle | VPS28 C-terminal domain-like | VPS28 C-terminal domain-like | automated matches | BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
C | d2j9uc_ | All alpha proteins | Four-helical up-and-down bundle | VPS28 C-terminal domain-like | VPS28 C-terminal domain-like | automated matches | BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
B | d2j9ub1 | Small proteins | Rubredoxin-like | Ran binding protein zinc finger-like | Ran binding protein zinc finger-like | Vacuolar protein-sorting-associated protein 36, VPS36 | BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
D | d2j9ud_ | Small proteins | Rubredoxin-like | Ran binding protein zinc finger-like | Ran binding protein zinc finger-like | automated matches | BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | VPS28 C-terminal domain-like | 8030691 | 4001213 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | VPS28 C-terminal domain-like | 8043070 | 3001082 | SCOP2 (2022-06-29) |
C | SCOP2B Superfamily | VPS28 C-terminal domain-like | 8043070 | 3001082 | SCOP2B (2022-06-29) |
B | SCOP2 Family | Ran binding protein zinc finger-like | 8003494 | 4000343 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | Ran binding protein zinc finger-like | 8003495 | 3000133 | SCOP2 (2022-06-29) |
D | SCOP2B Superfamily | Ran binding protein zinc finger-like | 8003495 | 3000133 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | VPS28_C | e2j9uA1 | A: alpha bundles | X: Four-helical up-and-down bundle | H: VPS28 C-terminal domain-like (From Topology) | T: VPS28 C-terminal domain-like | F: VPS28_C | ECOD (1.6) |
C | VPS28_C | e2j9uC1 | A: alpha bundles | X: Four-helical up-and-down bundle | H: VPS28 C-terminal domain-like (From Topology) | T: VPS28 C-terminal domain-like | F: VPS28_C | ECOD (1.6) |
B | Vps36-NZF-N | e2j9uB1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Vps36-NZF-N | ECOD (1.6) |
D | Vps36-NZF-N | e2j9uD1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Vps36-NZF-N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 1.20.120.1130 | Mainly Alpha | Up-down Bundle | Four Helix Bundle (Hemerythrin (Met), subunit A) | Vps28 C-terminal domain | CATH (4.3.0) |
C | 1.20.120.1130 | Mainly Alpha | Up-down Bundle | Four Helix Bundle (Hemerythrin (Met), subunit A) | Vps28 C-terminal domain | CATH (4.3.0) |
B | 2.30.30.380 | Mainly Beta | Roll | SH3 type barrels. | Zn-finger domain of Sec23/24 | CATH (4.3.0) |
D | 2.30.30.380 | Mainly Beta | Roll | SH3 type barrels. | Zn-finger domain of Sec23/24 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03997 | VPS28 protein (VPS28) | VPS28 protein | - | Family | |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR037206 | VPS28, C-terminal domain superfamily | Homologous Superfamily | |
IPR007143 | Vacuolar protein sorting-associated Vps28 | Family | |
IPR017899 | Vacuolar protein sorting-associated, VPS28, C-terminal | Domain | |
IPR017898 | Vacuolar protein sorting-associated, VPS28, N-terminal | Domain | |
IPR038358 | VPS28, N-terminal domain superfamily | Homologous Superfamily | |
IPR037202 | ESCRT assembly domain | Homologous Superfamily | |
IPR036443 | Zinc finger, RanBP2-type superfamily | Homologous Superfamily | |
IPR036388 | Winged helix-like DNA-binding domain superfamily | Homologous Superfamily | |
IPR036390 | Winged helix DNA-binding domain superfamily | Homologous Superfamily | |
IPR040608 | Snf8/Vps36 family | Family | |
IPR011993 | PH-like domain superfamily | Homologous Superfamily | |
IPR031558 | Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain | Domain | |
IPR001876 | Zinc finger, RanBP2-type | Domain | |
IPR021648 | Vacuolar protein sorting protein 36, GLUE domain | Domain | |
IPR037855 | Vacuolar protein sorting protein 36 | Family |