3cue Summary

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Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

The structure was published by Cai, Y., Chin, H.F., Lazarova, D., et al., De La Cruz, E.M., Ferro-Novick, S., and Reinisch, K.M., in 2008 in a paper entitled "The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.7 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This entry contains 28 copies of 5 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Transport protein particle 23 kDa subunit Q03784 (1-219) (TRS23_YEAST)search Saccharomyces cerevisiae S288csearch 100% 219 72%
G Transport protein particle 23 kDa subunit Q03784 (1-219) (TRS23_YEAST)search Saccharomyces cerevisiae S288csearch 100% 219 72%
M Transport protein particle 23 kDa subunit Q03784 (1-219) (TRS23_YEAST)search Saccharomyces cerevisiae S288csearch 100% 219 72%
S Transport protein particle 23 kDa subunit Q03784 (1-219) (TRS23_YEAST)search Saccharomyces cerevisiae S288csearch 100% 219 72%
B Transport protein particle 31 kDa subunit Q03337 (1-283) (TRS31_YEAST)search Saccharomyces cerevisiae S288csearch 100% 283 59%
H Transport protein particle 31 kDa subunit Q03337 (1-283) (TRS31_YEAST)search Saccharomyces cerevisiae S288csearch 100% 283 59%
N Transport protein particle 31 kDa subunit Q03337 (1-283) (TRS31_YEAST)search Saccharomyces cerevisiae S288csearch 100% 283 59%
T Transport protein particle 31 kDa subunit Q03337 (1-283) (TRS31_YEAST)search Saccharomyces cerevisiae S288csearch 100% 283 59%
C Transport protein particle 18 kDa subunit Q03630 (1-159) (BET5_YEAST)search Saccharomyces cerevisiae S288csearch 100% 159 89%
I Transport protein particle 18 kDa subunit Q03630 (1-159) (BET5_YEAST)search Saccharomyces cerevisiae S288csearch 100% 159 89%
O Transport protein particle 18 kDa subunit Q03630 (1-159) (BET5_YEAST)search Saccharomyces cerevisiae S288csearch 100% 159 89%
U Transport protein particle 18 kDa subunit Q03630 (1-159) (BET5_YEAST)search Saccharomyces cerevisiae S288csearch 100% 159 89%
D Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
E Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
J Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
K Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
P Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
Q Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
V Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
W Transport protein particle 22 kDa subunit P36149 (1-193) (BET3_YEAST)search Saccharomyces cerevisiae S288csearch 100% 193 97%
F GTP-binding protein YPT1 P01123 (1-206) (YPT1_YEAST)search Saccharomyces cerevisiae S288csearch 100% 206 80%
L GTP-binding protein YPT1 P01123 (1-206) (YPT1_YEAST)search Saccharomyces cerevisiae S288csearch 100% 206 80%
R GTP-binding protein YPT1 P01123 (1-206) (YPT1_YEAST)search Saccharomyces cerevisiae S288csearch 100% 206 80%
X GTP-binding protein YPT1 P01123 (1-206) (YPT1_YEAST)search Saccharomyces cerevisiae S288csearch 100% 206 80%


This entry contains 5 unique UniProt proteins:

UniProt accession Name Organism PDB
Q03784 (1 - 219) Transport protein particle 23 kDa subunit Saccharomyces cerevisiae
Q03337 (1 - 283) Transport protein particle 31 kDa subunit Saccharomyces cerevisiae
Q03630 (1 - 159) Transport protein particle 18 kDa subunit Saccharomyces cerevisiae
P36149 (1 - 193) Transport protein particle 22 kDa subunit Saccharomyces cerevisiae
P01123 (1 - 206) GTP-binding protein YPT1 Saccharomyces cerevisiae

Chain Structural classification (SCOP) Sequence family (Pfam)
A, G, M, S (Q03784) PF04099: Sybindin-like familysearch
B, H, N, T (Q03337) PF04051: Transport protein particle (TRAPP) componentsearch
C, I, O, U (Q03630) PF04099: Sybindin-like familysearch
D, E, J, K, P, Q, V, W (P36149) PF04051: Transport protein particle (TRAPP) componentsearch
F, L, R, X (P01123) G proteinssearch PF00071: Ras familysearch

Chain ID Biological process (GO) Cellular component (GO) Molecular function (GO)
A, G, M, S (Q03784) transportsearch ER to Golgi vesicle-mediated transportsearch positive regulation of Rab GTPase activitysearch autophagysearch chromosome organizationsearch vesicle-mediated transportsearch cis-Golgi networksearch endoplasmic reticulumsearch TRAPPII protein complexsearch TRAPPIII protein complexsearch pre-autophagosomal structuresearch Golgi apparatussearch TRAPPI protein complexsearch Rab guanyl-nucleotide exchange factor activitysearch protein bindingsearch
B, H, N, T (Q03337) autophagysearch ER to Golgi vesicle-mediated transportsearch positive regulation of Rab GTPase activitysearch transportsearch vesicle-mediated transportsearch endoplasmic reticulumsearch TRAPPII protein complexsearch TRAPPI protein complexsearch Golgi apparatussearch TRAPPIII protein complexsearch pre-autophagosomal structuresearch protein bindingsearch Rab guanyl-nucleotide exchange factor activitysearch
C, I, O, U (Q03630) transportsearch ER to Golgi vesicle-mediated transportsearch positive regulation of Rab GTPase activitysearch autophagysearch vesicle-mediated transportsearch cis-Golgi networksearch Golgi apparatussearch TRAPPI protein complexsearch TRAPPIII protein complexsearch endoplasmic reticulumsearch TRAPPII protein complexsearch pre-autophagosomal structuresearch protein bindingsearch Rab guanyl-nucleotide exchange factor activitysearch
D, E, J, K, P, Q, V, W (P36149) autophagysearch positive regulation of Rab GTPase activitysearch intra-Golgi vesicle-mediated transportsearch ER to Golgi vesicle-mediated transportsearch vesicle-mediated transportsearch transportsearch TRAPPI protein complexsearch Golgi apparatussearch TRAPPII protein complexsearch endoplasmic reticulumsearch TRAPPIII protein complexsearch cis-Golgi network membranesearch pre-autophagosomal structuresearch protein bindingsearch Rab guanyl-nucleotide exchange factor activitysearch identical protein bindingsearch
F, L, R, X (P01123) protein transportsearch small GTPase mediated signal transductionsearch Golgi vesicle buddingsearch SNARE complex disassemblysearch endocytic recyclingsearch ER to Golgi vesicle-mediated transportsearch CVT pathwaysearch pre-mRNA catabolic processsearch GTP catabolic processsearch COPII-coated vesicle buddingsearch retrograde vesicle-mediated transport, Golgi to ERsearch Golgi vesicle dockingsearch vesicle-mediated transportsearch transportsearch early endosome to Golgi transportsearch protein complex assemblysearch regulation of endoplasmic reticulum unfolded protein responsesearch macroautophagysearch Golgi stacksearch membranesearch Golgi membranesearch cytoplasmic vesiclesearch endoplasmic reticulumsearch cytoplasmsearch trans-Golgi networksearch pre-autophagosomal structuresearch endoplasmic reticulum membranesearch Golgi apparatussearch GTP bindingsearch nucleotide bindingsearch protein bindingsearch SNARE bindingsearch GTPase activitysearch

Chain InterPro annotation
A, G, M, S Sybindin-like proteinsearch Longin-like domainsearch
B, H, N, T Transport protein particle (TRAPP) componentsearch TRAPP I complex, subunit 5search NO signalling/Golgi transport ligand-binding domainsearch
C, I, O, U Sybindin-like proteinsearch Longin-like domainsearch
D, E, J, K, P, Q, V, W Transport protein particle (TRAPP) componentsearch TRAPP I complex, Bet3search NO signalling/Golgi transport ligand-binding domainsearch
F, L, R, X Small GTPase superfamilysearch Small GTPase superfamily, Rab typesearch Small GTP-binding protein domainsearch P-loop containing nucleoside triphosphate hydrolasesearch