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Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

Source organism: Saccharomyces cerevisiae S288C
Biochemical function: protein binding
Biological process: macroautophagy
Cellular component: cytosol

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GO terms

Sequence families

Pfam Protein families (Pfam)
PF04051
Domain description: Transport protein particle (TRAPP) component
Occurring in:
  1. Trafficking protein particle complex subunit 31
  2. Trafficking protein particle complex subunit BET3
The deposited structure of PDB entry 3cue contains 4 copies of Pfam domain PF04051 (Transport protein particle (TRAPP) component) in Trafficking protein particle complex subunit 31. Showing 1 copy in chain B.
The deposited structure of PDB entry 3cue contains 8 copies of Pfam domain PF04051 (Transport protein particle (TRAPP) component) in Trafficking protein particle complex subunit BET3. Showing 1 copy in chain W.

PF04099
Domain description: Sybindin-like family
Occurring in:
  1. Trafficking protein particle complex subunit 23
  2. Trafficking protein particle complex subunit BET5
The deposited structure of PDB entry 3cue contains 8 copies of Pfam domain PF04099 (Sybindin-like family) in Trafficking protein particle complex subunit 23. Showing 2 copies in chain A.
The deposited structure of PDB entry 3cue contains 4 copies of Pfam domain PF04099 (Sybindin-like family) in Trafficking protein particle complex subunit BET5. Showing 1 copy in chain U.

PF00071
Domain description: Ras family
Occurring in:
  1. GTP-binding protein YPT1
The deposited structure of PDB entry 3cue contains 4 copies of Pfam domain PF00071 (Ras family) in GTP-binding protein YPT1. Showing 1 copy in chain F.

InterPro InterPro annotations
IPR007233
Domain description: Trafficking protein particle complex subunit
Occurring in:
  1. Trafficking protein particle complex subunit 23
  2. Trafficking protein particle complex subunit BET5
IPR016721
Domain description: Bet3 family
Occurring in:
  1. Trafficking protein particle complex subunit BET3
IPR001806
Domain description: Small GTPase
Occurring in:
  1. GTP-binding protein YPT1
IPR007194
Domain description: Transport protein particle (TRAPP) component
Occurring in:
  1. Trafficking protein particle complex subunit 31
  2. Trafficking protein particle complex subunit BET3
IPR024096
Domain description: NO signalling/Golgi transport ligand-binding domain superfamily
Occurring in:
  1. Trafficking protein particle complex subunit 31
  2. Trafficking protein particle complex subunit BET3
IPR016696
Domain description: TRAPP I complex, subunit 5
Occurring in:
  1. Trafficking protein particle complex subunit 31
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. GTP-binding protein YPT1
IPR011012
Domain description: Longin-like domain superfamily
Occurring in:
  1. Trafficking protein particle complex subunit 23
  2. Trafficking protein particle complex subunit BET5
IPR005225
Domain description: Small GTP-binding protein domain
Occurring in:
  1. GTP-binding protein YPT1

Structure domains

CATH CATH domains
3.30.1380.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homology: Trafficking protein particle complex subunit 3
Occurring in:
  1. Trafficking protein particle complex subunit 31
  2. Trafficking protein particle complex subunit BET3
The deposited structure of PDB entry 3cue contains 4 copies of CATH domain 3.30.1380.20 (Muramoyl-pentapeptide Carboxypeptidase; domain 2) in Trafficking protein particle complex subunit 31. Showing 1 copy in chain B.
The deposited structure of PDB entry 3cue contains 8 copies of CATH domain 3.30.1380.20 (Muramoyl-pentapeptide Carboxypeptidase; domain 2) in Trafficking protein particle complex subunit BET3. Showing 1 copy in chain E.
3.30.450.70
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Beta-Lactamase
Homology: Beta-Lactamase
Occurring in:
  1. Trafficking protein particle complex subunit 23
  2. Trafficking protein particle complex subunit BET5
The deposited structure of PDB entry 3cue contains 4 copies of CATH domain 3.30.450.70 (Beta-Lactamase) in Trafficking protein particle complex subunit 23. Showing 1 copy in chain A.
The deposited structure of PDB entry 3cue contains 4 copies of CATH domain 3.30.450.70 (Beta-Lactamase) in Trafficking protein particle complex subunit BET5. Showing 1 copy in chain C.
3.40.50.300
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: P-loop containing nucleotide triphosphate hydrolases
Occurring in:
  1. GTP-binding protein YPT1
The deposited structure of PDB entry 3cue contains 4 copies of CATH domain 3.40.50.300 (Rossmann fold) in GTP-binding protein YPT1. Showing 1 copy in chain F.
SCOP SCOP annotation
52592
Class: Alpha and beta proteins (a/b)
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Occurring in:
  1. GTP-binding protein YPT1
The deposited structure of PDB entry 3cue contains 4 copies of SCOP domain 52592 (G proteins) in GTP-binding protein YPT1. Showing 1 copy in chain F.

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