SMTL ID : 7u06.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-4-2-2-2-2-1-2-2-2-2-mer

Ligands

4 x PLM: PALMITIC ACID(Covalent)

PLM.1: 28 residues within 4Å: Chain C: V.44, L.48 Chain D: F.30, I.63, L.67, I.68, F.71, L.72, L.77, P.78, C.80, T.86, V.89, L.90, A.94, F.95, F.98, L.99, L.124, I.143, L.144, V.147, L.148, S.151, L.152, V.155, L.157 Chain E: A.83 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.67, D:I.68, D:F.71, D:F.71, D:V.89, D:L.90, D:F.95, D:F.98, D:L.99, D:V.147, D:L.152, C:V.44 Hydrogen bonds: D:C.80 PLM.2: 26 residues within 4Å: Chain G: F.30, I.63, L.67, I.68, F.71, L.77, R.79, C.80, T.86, V.89, L.90, A.94, F.95, F.98, L.99, I.143, L.144, V.147, L.148, S.151, L.152, V.155, L.157 Chain H: A.61, F.64, L.65 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.67, G:F.71, G:F.71, G:L.90, G:A.94, G:V.147 Hydrogen bonds: G:C.80 PLM.3: 26 residues within 4Å: Chain O: V.44 Chain P: F.30, I.63, L.67, I.68, F.71, L.72, L.77, P.78, C.80, T.86, V.89, L.90, A.94, F.95, F.98, L.99, L.124, I.143, L.144, V.147, L.148, S.151, L.152, V.155, L.157 14 PLIP interactions: 14 interactions with chain P Hydrophobic interactions: P:F.30, P:L.67, P:I.68, P:F.71, P:F.71, P:V.89, P:L.90, P:A.94, P:F.98, P:L.99, P:L.144, P:V.147, P:V.155 Hydrogen bonds: P:C.80 PLM.4: 28 residues within 4Å: Chain S: F.30, I.63, L.67, I.68, F.71, L.72, L.77, R.79, C.80, T.86, V.89, L.90, A.94, F.95, F.98, L.99, L.124, I.143, L.144, V.147, L.148, S.151, L.152, V.155, L.157 Chain T: A.61, F.64, L.65 3 PLIP interactions: 3 interactions with chain S Hydrophobic interactions: S:A.94, S:L.152 Hydrogen bonds: S:C.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bagde, S.R. et al., Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms. Sci Adv (2022)

Release Date

2022-04-27

Peptides

Trafficking protein particle complex II-specific subunit 65: AM
TRAPP-associated protein TCA17: BN
Trafficking protein particle complex subunit 33: CO
Trafficking protein particle complex subunit BET3: DGPS
Trafficking protein particle complex subunit BET5: EQ
Trafficking protein particle complex subunit 23: FR
Trafficking protein particle complex subunit 31: HT
Trafficking protein particle complex subunit 20: IU
GTP-binding protein YPT32/YPT11: J
Trafficking protein particle complex II-specific subunit 130: KV
Trafficking protein particle complex II-specific subunit 120: LW
Trafficking protein particle complex II-specific subunit 130: XY
Trafficking protein particle complex II-specific subunit 65: Z0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

M
c

B
D

N
d

C
E

O
e

D
F

G
I

P
f

S
i

E
G

Q
g

F
H

R
h

H
J

T
j

I
K

U
k

J
l

K
B

V
b

L
A

W
a

X
M

Y
m

Z
n

0
N

Trafficking protein particle complex II-specific subunit 65

TRAPP-associated protein TCA17

Trafficking protein particle complex subunit 33

Trafficking protein particle complex subunit BET3

Trafficking protein particle complex subunit BET5

Trafficking protein particle complex subunit 23

Trafficking protein particle complex subunit 31

Trafficking protein particle complex subunit 20

GTP-binding protein YPT32/YPT11

Trafficking protein particle complex II-specific subunit 130

Trafficking protein particle complex II-specific subunit 120

Trafficking protein particle complex II-specific subunit 130

Trafficking protein particle complex II-specific subunit 65

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