7U06 | pdb_00007u06

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

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
J [auth l]SCOP2B SuperfamilyRas-like P-loop GTPases 8056347 3002022 SCOP2B (2022-06-29)
R [auth h]SCOP2B SuperfamilySNARE-like 8090320 3001113 SCOP2B (2022-06-29)
F [auth H]SCOP2B SuperfamilySNARE-like 8090320 3001113 SCOP2B (2022-06-29)
Q [auth g]SCOP2B SuperfamilySNARE-like 8090321 3001113 SCOP2B (2022-06-29)
E [auth G]SCOP2B SuperfamilySNARE-like 8090321 3001113 SCOP2B (2022-06-29)
S [auth i]SCOP2B SuperfamilyLigand-binding domain in the NO signalling and Golgi transport 8065542 3001668 SCOP2B (2022-06-29)
P [auth f]SCOP2B SuperfamilyLigand-binding domain in the NO signalling and Golgi transport 8065542 3001668 SCOP2B (2022-06-29)
G [auth I]SCOP2B SuperfamilyLigand-binding domain in the NO signalling and Golgi transport 8065542 3001668 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyLigand-binding domain in the NO signalling and Golgi transport 8065542 3001668 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
J [auth l]Rase7u06l1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: RasECOD (1.6)
U [auth k]Sedlin_Ne7u06k1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: Sedlin_NECOD (1.6)
I [auth K]Sedlin_Ne7u06K1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: Sedlin_NECOD (1.6)
R [auth h]Sybindine7u06h1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: SybindinECOD (1.6)
F [auth H]Sybindine7u06H1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: SybindinECOD (1.6)
Q [auth g]Sybindine7u06g1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: SybindinECOD (1.6)
E [auth G]Sybindine7u06G1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: SybindinECOD (1.6)
S [auth i]TRAPPe7u06i1 A: a+b complex topologyX: H-NOX domain (From Topology)H: H-NOX domain (From Topology)T: H-NOX domainF: TRAPPECOD (1.6)
P [auth f]TRAPPe7u06f1 A: a+b complex topologyX: H-NOX domain (From Topology)H: H-NOX domain (From Topology)T: H-NOX domainF: TRAPPECOD (1.6)
G [auth I]TRAPPe7u06I1 A: a+b complex topologyX: H-NOX domain (From Topology)H: H-NOX domain (From Topology)T: H-NOX domainF: TRAPPECOD (1.6)
D [auth F]TRAPPe7u06F1 A: a+b complex topologyX: H-NOX domain (From Topology)H: H-NOX domain (From Topology)T: H-NOX domainF: TRAPPECOD (1.6)
O [auth e]TRAPPe7u06e1 A: a+b complex topologyX: H-NOX domain (From Topology)H: H-NOX domain (From Topology)T: H-NOX domainF: TRAPPECOD (1.6)
N [auth d]Sedlin_Ne7u06d1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: Sedlin_NECOD (1.6)
B [auth D]Sedlin_Ne7u06D1 A: a+b three layersX: Profilin-likeH: profilin-like (From Topology)T: profilin-likeF: Sedlin_NECOD (1.6)
M [auth c]F_UNCLASSIFIEDe7u06c1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: F_UNCLASSIFIEDECOD (1.6)
A [auth C]F_UNCLASSIFIEDe7u06C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: F_UNCLASSIFIEDECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth K],
U [auth k]		PF04628Sedlin, N-terminal conserved region (Sedlin_N)Sedlin, N-terminal conserved region- Family
H [auth J],
T [auth j]		PF04051Transport protein particle (TRAPP) component (TRAPP)Transport protein particle (TRAPP) component- Family
F [auth H],
R [auth h]		PF04099Sybindin-like family (Sybindin)Sybindin-like family- Family
E [auth G],
Q [auth g]		PF04099Sybindin-like family (Sybindin)Sybindin-like family- Family
D [auth F],
G [auth I],
P [auth f],
S [auth i]		PF04051Transport protein particle (TRAPP) component (TRAPP)Transport protein particle (TRAPP) component- Family
C [auth E],
O [auth e]		PF04051Transport protein particle (TRAPP) component (TRAPP)Transport protein particle (TRAPP) component- Family
B [auth D],
N [auth d]		PF04628Sedlin, N-terminal conserved region (Sedlin_N)Sedlin, N-terminal conserved region- Family
L [auth A],
W [auth a]		PF08626Trs120/TRAPPC9, N-terminal domain (TRAPPC9-Trs120)Trs120/TRAPPC9, N-terminal domainThis region is found at the N-terminal of Saccharomyces cerevisiae Trs120 protein (Swiss:Q04183). Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic [1]. Trs120 is specific to the ...This region is found at the N-terminal of Saccharomyces cerevisiae Trs120 protein (Swiss:Q04183). Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic [1]. Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way [2]. It is likely that there is a complex function for TRAPP II in multiple pathways [3].
Domain
K [auth B],
V [auth b]		PF12584Trafficking protein particle complex subunit 10, TRAPPC10 (TRAPPC10)Trafficking protein particle complex subunit 10, TRAPPC10- Family
A [auth C],
M [auth c]		PF12735TRAPP trafficking subunit Trs65 IgD3 (IgD3_Trs65)TRAPP trafficking subunit Trs65 IgD3This entry includes Trp65, an essential subunit of the TRAPP Golgi trafficking complex [1-5]. TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII [5] and they function in various vesicle trafficking pathways. TRAPPI media ...This entry includes Trp65, an essential subunit of the TRAPP Golgi trafficking complex [1-5]. TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII [5] and they function in various vesicle trafficking pathways. TRAPPI mediates transport from endoplasmic reticulum to cis-Golgi by tethering COPII-coated vesicles; TRAPPII interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport, and TRAPPIII plays a unique role in autophagy. TRAPP complexes act as GEFs and play an essential role in catalysing nucleotide exchange for Ypt/Rab GTPase. The three complexes share a core of six different proteins (Bet3, Bet5, Trs20, Trs23, Trs31, and Trs33) that make up core TRAPPI. TRAPPII contains four additional proteins (Trs120, Trs130, Trs65, and Tca17), and TRAPPIII has one additional Trs85 in yeast [5]. while Trp65 has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPPII is supported by the findings that the protein co-localises with Trs130p, and deletion of Trs65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPPII-specific subunits is modified [4]. Trs65 is essential to the formation of TRAPPII dimer and consists of three Ig-like domains (IgD1, IgD2 and IgD3). This entry represents IgD3 domain of Trs65 [5].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
J [auth l]GTP-binding protein YPT32/YPT11
I [auth K],
U [auth k]		Trafficking protein particle complex subunit 20-
H [auth J],
T [auth j]		Trafficking protein particle complex subunit 31-
F [auth H],
R [auth h]		Trafficking protein particle complex subunit 23-
E [auth G],
Q [auth g]		Trafficking protein particle complex subunit BET5-
D [auth F],
G [auth I],
P [auth f],
S [auth i]		Trafficking protein particle complex subunit BET3-
C [auth E],
O [auth e]		Trafficking protein particle complex subunit 33-
B [auth D],
N [auth d]		TRAPP-associated protein TCA17-
AA [auth N],
Z [auth n]		Trafficking protein particle complex II-specific subunit 65---
X [auth M],
Y [auth m]		Trafficking protein particle complex II-specific subunit 130---
L [auth A],
W [auth a]		Trafficking protein particle complex II-specific subunit 120-
K [auth B],
V [auth b]		Trafficking protein particle complex II-specific subunit 130-
A [auth C],
M [auth c]		Trafficking protein particle complex II-specific subunit 65-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth l]IPR005225Small GTP-binding domainDomain
J [auth l]IPR001806Small GTPaseFamily
J [auth l]IPR050209Rab GTPases family involved in membrane traffickingFamily
J [auth l]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
I [auth K],
U [auth k]		IPR011012Longin-like domain superfamilyHomologous Superfamily
I [auth K],
U [auth k]		IPR006722Trafficking protein particle complex subunit 2Family
H [auth J],
T [auth j]		IPR024096NO signalling/Golgi transport ligand-binding domain superfamilyHomologous Superfamily
H [auth J],
T [auth j]		IPR016696TRAPP I complex, subunit 5Family
H [auth J],
T [auth j]		IPR007194Transport protein particle (TRAPP) componentFamily
F [auth H],
R [auth h]		IPR007233Trafficking protein particle complex subunitFamily
F [auth H],
R [auth h]		IPR011012Longin-like domain superfamilyHomologous Superfamily
E [auth G],
Q [auth g]		IPR007233Trafficking protein particle complex subunitFamily
E [auth G],
Q [auth g]		IPR011012Longin-like domain superfamilyHomologous Superfamily
D [auth F],
G [auth I],
P [auth f],
S [auth i]		IPR024096NO signalling/Golgi transport ligand-binding domain superfamilyHomologous Superfamily
D [auth F],
G [auth I],
P [auth f],
S [auth i]		IPR007194Transport protein particle (TRAPP) componentFamily
D [auth F],
G [auth I],
P [auth f],
S [auth i]		IPR016721Bet3 familyFamily
C [auth E],
O [auth e]		IPR024096NO signalling/Golgi transport ligand-binding domain superfamilyHomologous Superfamily
C [auth E],
O [auth e]		IPR007194Transport protein particle (TRAPP) componentFamily
C [auth E],
O [auth e]		IPR037992TRAPP complex, Trs33 subunitFamily
B [auth D],
N [auth d]		IPR011012Longin-like domain superfamilyHomologous Superfamily
B [auth D],
N [auth d]		IPR006722Trafficking protein particle complex subunit 2Family
L [auth A],
W [auth a]		IPR013935Trs120/TRAPPC9Family
K [auth B],
V [auth b]		IPR056915Trs130, second Ig-like domainDomain
K [auth B],
V [auth b]		IPR022233TRAPPC10/Trs130, C-terminalDomain
K [auth B],
V [auth b]		IPR056916Trs130, NTS domainDomain
K [auth B],
V [auth b]		IPR045126Trafficking protein particle complex subunit TRAPPC10/Trs130Family
K [auth B],
V [auth b]		IPR056913TRAPPC10/Trs130, N-terminalDomain
A [auth C],
M [auth c]		IPR055426Trafficking protein particle complex II-specific subunit 65, IgD2Domain
A [auth C],
M [auth c]		IPR024662Trafficking protein particle complex II-specific subunit 65Family
A [auth C],
M [auth c]		IPR055425Trafficking protein particle complex II-specific subunit 65, IgD1Domain
A [auth C],
M [auth c]		IPR055420Trafficking protein particle complex II-specific subunit 65, IgD3Domain