› 7u05

Electron Microscopy
3.7Å resolution

Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure)

Released:
DOI: 10.2210/pdb7u05/pdb
PDB entry 7u05 coloured by chain, front view.
PDB entry 7u05 coloured by chain, side view.
PDB entry 7u05 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms.
Bagde SR, Fromme JC
OpenAccess logo Sci Adv 8 eabn7446 (2022)
PMID: 35559680
Related structures: EMD-26254

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152404 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Trafficking protein particle complex II-specific subunit 130 Chains: M, m
Molecule details ›
Chains: M, m
Length: 242 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae
Trafficking protein particle complex II-specific subunit 65 Chains: C, c
Molecule details ›
Chains: C, c
Length: 560 amino acids
Theoretical weight: 63.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32893 (Residues: 1-560; Coverage: 100%)
Gene names: KRE11, TRS65, YGR166W
Sequence domains: TRAPP trafficking subunit Trs65
TRAPP-associated protein TCA17 Chains: D, d
Molecule details ›
Chains: D, d
Length: 152 amino acids
Theoretical weight: 17.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32613 (Residues: 1-152; Coverage: 100%)
Gene names: SYGP-ORF36, TCA17, YEL048C
Sequence domains: Sedlin, N-terminal conserved region
Trafficking protein particle complex subunit 33 Chains: E, e
Molecule details ›
Chains: E, e
Length: 268 amino acids
Theoretical weight: 30.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q99394 (Residues: 1-268; Coverage: 100%)
Gene names: O3251, TRS33, YOR115C, YOR3251C
Sequence domains: Transport protein particle (TRAPP) component
Trafficking protein particle complex subunit BET3 Chains: F, I, f, i
Molecule details ›
Chains: F, I, f, i
Length: 193 amino acids
Theoretical weight: 22.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36149 (Residues: 1-193; Coverage: 100%)
Gene names: BET3, YKR068C
Sequence domains: Transport protein particle (TRAPP) component
Trafficking protein particle complex subunit BET5 Chains: G, g
Molecule details ›
Chains: G, g
Length: 159 amino acids
Theoretical weight: 18.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03630 (Residues: 1-159; Coverage: 100%)
Gene names: BET5, YML077W
Sequence domains: Sybindin-like family
Trafficking protein particle complex subunit 23 Chains: H, h
Molecule details ›
Chains: H, h
Length: 219 amino acids
Theoretical weight: 24.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03784 (Residues: 1-219; Coverage: 100%)
Gene names: TRS23, YD8419.13, YDR246W
Sequence domains: Sybindin-like family
Trafficking protein particle complex subunit 31 Chains: J, j
Molecule details ›
Chains: J, j
Length: 283 amino acids
Theoretical weight: 31.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03337 (Residues: 1-283; Coverage: 100%)
Gene names: TRS31, YDR472W
Sequence domains: Transport protein particle (TRAPP) component
Trafficking protein particle complex subunit 20 Chains: K, k
Molecule details ›
Chains: K, k
Length: 175 amino acids
Theoretical weight: 19.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38334 (Residues: 1-175; Coverage: 100%)
Gene names: TRS20, YBR1722, YBR254C
Sequence domains: Sedlin, N-terminal conserved region
GTP-binding protein YPT32/YPT11 Chains: L, l
Molecule details ›
Chains: L, l
Length: 227 amino acids
Theoretical weight: 25.31 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P51996 (Residues: 1-220; Coverage: 99%)
Gene names: YGL210W, YPT11, YPT32
Sequence domains: Ras family
Trafficking protein particle complex II-specific subunit 130 Chains: B, b
Molecule details ›
Chains: B, b
Length: 1104 amino acids
Theoretical weight: 128.42 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03660 (Residues: 1-1102; Coverage: 100%)
Gene names: TRS130, YM8261.12C, YMR218C
Sequence domains: Trafficking protein particle complex subunit 10, TRAPPC10
Trafficking protein particle complex II-specific subunit 120 Chains: A, a
Molecule details ›
Chains: A, a
Length: 1289 amino acids
Theoretical weight: 147.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04183 (Residues: 1-1289; Coverage: 100%)
Gene names: D9509.25, ESBP10, TRS120, YDR407C
Sequence domains: Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
Trafficking protein particle complex II-specific subunit 65 Chains: N, n
Molecule details ›
Chains: N, n
Length: 210 amino acids
Theoretical weight: 17.89 KDa
Source organism: Saccharomyces cerevisiae

Ligands and Environments

1 bound ligand:
Ligand PLM 4 x PLM
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-26254
Expression system: Escherichia coli BL21

Quick links

Citations

2 review citations

The TRAPP complexes: discriminating GTPases in context.
Bagde et al. (2023)
1 more