SMTL ID : 7ylx.1

yeast TRiC-plp2-actin complex at S4 closed TRiC state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.162, S.165, S.166, G.422, V.517, E.519 Ligands: MG.2, AF3.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.45, A:G.97, A:T.98, A:T.99, A:T.99, A:T.99, A:S.100, A:S.165, A:S.166, A:G.422, A:E.519 Salt bridges: A:K.167 ADP.4: 18 residues within 4Å: Chain B: L.37, G.38, P.39, D.90, G.91, T.92, T.93, S.94, S.162, S.163, G.404, L.444, L.472, L.474, I.487, E.489 Ligands: MG.5, AF3.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.38, B:G.91, B:T.93, B:S.94, B:S.162, B:S.163, B:G.404, B:E.489 Salt bridges: B:K.164 ADP.7: 17 residues within 4Å: Chain C: G.40, P.41, D.91, G.92, T.93, T.94, T.156, S.159, S.160, K.161, G.414, I.482, V.484, I.497, Q.499 Ligands: MG.8, AF3.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.40, C:G.92, C:T.93, C:T.93, C:T.94, C:S.160, C:G.414, C:G.415 Salt bridges: C:K.161 ADP.10: 18 residues within 4Å: Chain D: L.65, G.66, D.86, D.117, G.118, T.119, T.120, G.121, T.186, S.190, G.443, L.515, M.522, V.527, D.529, K.534 Ligands: MG.11, AF3.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.66, D:G.118, D:T.119, D:T.120, D:G.121, D:S.190, D:G.443, D:D.529, D:K.534 ADP.13: 19 residues within 4Å: Chain E: L.39, D.91, G.92, T.93, T.94, T.95, S.158, T.161, G.476, G.477, I.512, L.516, I.544, G.546, Y.557, E.561, K.566 Ligands: MG.14, AF3.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.92, E:T.93, E:T.94, E:T.94, E:T.95, E:T.95, E:T.95, E:G.476, E:G.477, E:G.546, E:Y.557, E:K.566, E:K.566 ADP.16: 19 residues within 4Å: Chain F: G.45, D.96, G.97, T.99, S.100, T.164, A.165, S.167, S.168, G.412, G.413, G.414, I.449, F.483, V.496, E.498, K.503 Ligands: MG.17, AF3.18 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:T.43, F:G.45, F:G.97, F:T.99, F:T.99, F:T.99, F:S.100, F:T.164, F:S.167, F:S.168, F:G.413, F:G.414, F:E.498, F:K.503 ADP.20: 17 residues within 4Å: Chain G: G.47, P.48, D.98, G.99, T.100, N.101, V.166, S.168, S.169, K.170, G.422, A.423, L.463, I.501, I.517, D.519 Ligands: MG.19 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.47, G:D.98, G:G.99, G:T.100, G:N.101, G:S.168, G:S.169, G:A.423, G:D.519 Salt bridges: G:K.170, G:K.170 ADP.21: 15 residues within 4Å: Chain H: L.37, D.89, G.90, T.91, T.92, T.93, S.156, T.160, G.414, A.415, L.458, V.491, I.506 Ligands: MG.22, AF3.23 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.90, H:T.91, H:T.92, H:T.92, H:T.92, H:T.93, H:A.415 ADP.24: 19 residues within 4Å: Chain I: S.43, G.45, P.46, N.64, D.65, D.96, T.99, T.162, S.165, S.166, K.167, G.421, G.422, G.423, L.502, V.517, E.519 Ligands: MG.25, AF3.26 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:D.65, I:D.65, I:D.65, I:S.165, I:S.165, I:S.166, I:G.422, I:G.423 Salt bridges: I:K.167 ADP.27: 20 residues within 4Å: Chain J: T.36, L.37, D.90, G.91, T.93, S.94, T.159, S.162, S.163, K.164, G.403, G.404, G.405, E.408, L.444, L.472, I.487, E.489 Ligands: MG.28, AF3.29 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:G.91, J:T.93, J:T.93, J:S.94, J:S.162, J:S.163, J:G.404, J:G.405 Salt bridges: J:K.164, J:K.164 ADP.30: 19 residues within 4Å: Chain K: G.40, P.41, D.91, G.92, T.93, T.94, S.95, T.156, S.157, L.158, S.159, G.413, G.414, G.415, I.482, I.497, Q.499 Ligands: MG.31, AF3.32 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.40, K:D.60, K:G.92, K:T.93, K:T.94, K:T.156, K:L.158, K:S.159, K:S.159, K:G.414, K:G.415, K:Q.499, K:Q.499 Salt bridges: K:K.161 ADP.33: 15 residues within 4Å: Chain L: L.65, G.66, P.67, D.117, G.118, T.119, T.120, G.121, S.190, G.442, G.443, L.515, D.529 Ligands: MG.34, AF3.35 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:G.66, L:G.118, L:T.119, L:T.120, L:T.120, L:T.120, L:T.120, L:G.121, L:S.190, L:D.529 Salt bridges: L:K.191, L:K.191 ADP.36: 20 residues within 4Å: Chain M: L.39, P.41, D.91, G.92, T.93, T.94, T.95, S.158, T.161, K.162, G.475, G.476, L.516, I.544, D.545, G.546, I.559, E.561 Ligands: MG.37, AF3.38 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:G.92, M:T.94, M:T.94, M:T.94, M:T.94, M:T.95, M:G.476, M:D.545, M:G.546, M:E.561 Salt bridges: M:K.162 ADP.39: 18 residues within 4Å: Chain N: L.44, G.45, P.46, D.96, G.97, T.99, T.164, S.167, S.168, G.412, G.413, G.414, L.453, V.481, V.496, E.498 Ligands: MG.40, AF3.41 7 PLIP interactions: 7 interactions with chain N Hydrogen bonds: N:G.97, N:S.167, N:S.168, N:S.168, N:G.413, N:G.414, N:E.498 ADP.42: 17 residues within 4Å: Chain P: M.46, P.48, D.98, G.99, N.101, L.102, S.168, S.169, Y.172, G.422, A.423, L.463, V.499, I.501, I.517, D.519 Ligands: MG.43 7 PLIP interactions: 7 interactions with chain P Hydrogen bonds: P:G.99, P:L.102, P:S.168, P:S.169, P:A.423, P:D.519 Salt bridges: P:K.170 ADP.44: 15 residues within 4Å: Chain Q: L.37, D.89, G.90, T.91, T.92, S.156, T.160, G.414, A.415, G.416, L.458, V.491, D.508 Ligands: MG.45, AF3.46 10 PLIP interactions: 10 interactions with chain Q Hydrogen bonds: Q:G.90, Q:T.91, Q:T.91, Q:T.92, Q:T.160, Q:A.415, Q:G.416, Q:D.508 Salt bridges: Q:K.161, Q:K.161

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.96 Ligands: ADP.1, AF3.3 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: D.90, K.164 Ligands: ADP.4, AF3.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.90 MG.8: 4 residues within 4Å: Chain C: D.91, S.157, S.160 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.91, C:S.157 MG.11: 3 residues within 4Å: Chain D: D.117 Ligands: ADP.10, AF3.12 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain E: D.91, S.158 Ligands: ADP.13, AF3.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.91 MG.17: 3 residues within 4Å: Chain F: D.96 Ligands: ADP.16, AF3.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.96 MG.19: 3 residues within 4Å: Chain G: D.98, V.166 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain H: D.89 Ligands: ADP.21, AF3.23 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.89 MG.25: 3 residues within 4Å: Chain I: D.96 Ligands: ADP.24, AF3.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.96, I:D.96 MG.28: 6 residues within 4Å: Chain J: D.90, T.160, S.163, K.164 Ligands: ADP.27, AF3.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.90, J:D.90 MG.31: 3 residues within 4Å: Chain K: D.91, S.157 Ligands: ADP.30 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.91, K:S.157 MG.34: 4 residues within 4Å: Chain L: D.117, K.191 Ligands: ADP.33, AF3.35 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.117 MG.37: 5 residues within 4Å: Chain M: D.91, G.92, K.162 Ligands: ADP.36, AF3.38 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.91 MG.40: 3 residues within 4Å: Chain N: D.96 Ligands: ADP.39, AF3.41 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.96 MG.43: 3 residues within 4Å: Chain P: D.98, S.169 Ligands: ADP.42 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.98 MG.45: 5 residues within 4Å: Chain Q: D.89, T.160, K.161 Ligands: ADP.44, AF3.46 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.89, Q:D.89

14 x AF3: ALUMINUM FLUORIDE(Non-covalent)(Covalent)

AF3.3: 9 residues within 4Å: Chain A: N.64, D.65, G.66, T.98, T.99, K.167, D.404 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) AF3.6: 10 residues within 4Å: Chain B: D.59, G.89, D.90, G.91, T.92, T.93, K.164, D.386 Ligands: ADP.4, MG.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.59 AF3.9: 8 residues within 4Å: Chain C: N.59, D.60, G.61, T.93, T.94, K.161, D.396 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.60, C:T.93 AF3.12: 7 residues within 4Å: Chain D: D.86, G.87, T.119, K.191, D.425 Ligands: ADP.10, MG.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 AF3.15: 9 residues within 4Å: Chain E: D.60, D.91, G.92, T.93, T.94, K.162, D.458 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) AF3.18: 13 residues within 4Å: Chain F: N.64, D.65, G.66, G.95, D.96, G.97, T.98, T.99, S.168, K.169, D.395 Ligands: ADP.16, MG.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.65 AF3.23: 7 residues within 4Å: Chain H: D.58, G.59, T.91, K.161, D.397 Ligands: ADP.21, MG.22 No protein-ligand interaction detected (PLIP) AF3.26: 10 residues within 4Å: Chain I: D.65, G.95, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: ADP.24, MG.25 No protein-ligand interaction detected (PLIP) AF3.29: 9 residues within 4Å: Chain J: D.59, G.89, D.90, G.91, T.92, K.164, D.386 Ligands: ADP.27, MG.28 No protein-ligand interaction detected (PLIP) AF3.32: 8 residues within 4Å: Chain K: N.59, D.60, G.61, T.93, T.94, K.161, D.396 Ligands: ADP.30 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.60 AF3.35: 9 residues within 4Å: Chain L: N.85, D.86, G.87, D.117, T.119, K.191, D.425 Ligands: ADP.33, MG.34 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.86 AF3.38: 9 residues within 4Å: Chain M: D.60, G.61, D.91, G.92, T.93, T.94, K.162 Ligands: ADP.36, MG.37 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.60 AF3.41: 8 residues within 4Å: Chain N: D.65, G.95, D.96, T.98, K.169, D.395 Ligands: ADP.39, MG.40 No protein-ligand interaction detected (PLIP) AF3.46: 9 residues within 4Å: Chain Q: D.58, G.59, G.88, D.89, T.91, K.161, D.397 Ligands: ADP.44, MG.45 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, W. et al., Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. Sci Adv (2023)

Release Date

2023-03-29

Peptides

T-complex protein 1 subunit alpha: AI
T-complex protein 1 subunit beta: BJ
T-complex protein 1 subunit delta: CK
T-complex protein 1 subunit epsilon: DL
T-complex protein 1 subunit gamma: EM
T-complex protein 1 subunit eta: FN
T-complex protein 1 subunit theta: GP
T-complex protein 1 subunit zeta: HQ
Phosducin-like protein 2: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
a

B
B

J
b

C
D

K
d

D
E

L
e

E
G

M
g

F
H

N
h

G
Q

P
q

H
Z

Q
z

O
p

T-complex protein 1 subunit alpha

T-complex protein 1 subunit beta

T-complex protein 1 subunit delta

T-complex protein 1 subunit epsilon

T-complex protein 1 subunit gamma

T-complex protein 1 subunit eta

T-complex protein 1 subunit theta

T-complex protein 1 subunit zeta

Phosducin-like protein 2

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