SMTL ID : 9e2s.1

Apo TRiC in closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.99 Ligands: ADP.2, AF3.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.99 MG.4: 3 residues within 4Å: Chain B: D.92 Ligands: ADP.5, AF3.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.92 MG.8: 4 residues within 4Å: Chain C: D.104, T.172 Ligands: AF3.7, ADP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.104 MG.12: 4 residues within 4Å: Chain D: D.97, K.170 Ligands: AF3.10, ADP.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.97, D:D.97 MG.13: 3 residues within 4Å: Chain E: D.104 Ligands: ADP.14, AF3.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.104, E:D.104 MG.17: 3 residues within 4Å: Chain F: D.88 Ligands: AF3.16, ADP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.88 MG.19: 3 residues within 4Å: Chain G: D.93 Ligands: ADP.20, AF3.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.93 MG.24: 5 residues within 4Å: Chain H: D.90, T.158, K.159 Ligands: AF3.22, ADP.23 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.90 MG.27: 4 residues within 4Å: Chain I: D.99, K.171 Ligands: AF3.25, ADP.26 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.99 MG.28: 4 residues within 4Å: Chain J: D.92, K.166 Ligands: ADP.29, AF3.30 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.92 MG.32: 4 residues within 4Å: Chain K: D.104, G.105 Ligands: ADP.31, AF3.33 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.104 MG.36: 4 residues within 4Å: Chain L: D.97, K.170 Ligands: ADP.34, AF3.35 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.97 MG.39: 3 residues within 4Å: Chain M: D.104 Ligands: AF3.37, ADP.38 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.104 MG.42: 3 residues within 4Å: Chain N: D.88 Ligands: ADP.40, AF3.41 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.88 MG.43: 3 residues within 4Å: Chain O: D.93 Ligands: AF3.44, ADP.45 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.93 MG.47: 3 residues within 4Å: Chain P: D.90 Ligands: AF3.46, ADP.48 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.90

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

ADP.2: 14 residues within 4Å: Chain A: Y.47, G.48, P.49, D.99, G.100, T.101, F.103, T.166, M.169, S.170, G.412, I.497 Ligands: MG.1, AF3.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.47, A:Y.47, A:T.101, A:S.170, A:G.412 ADP.5: 17 residues within 4Å: Chain B: L.40, D.92, G.93, T.94, T.95, S.96, T.161, S.164, S.165, G.408, G.409, N.497, V.502, E.504, R.509 Ligands: MG.4, AF3.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.94, B:T.95, B:T.95, B:T.95, B:S.164, B:S.164, B:S.165, B:G.409, B:E.504, B:R.509 Salt bridges: B:K.166 ADP.9: 17 residues within 4Å: Chain C: L.52, G.53, P.54, D.104, G.105, T.107, T.172, S.175, G.422, L.462, L.494, M.501, Q.504, V.506, E.508 Ligands: AF3.7, MG.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.53, C:G.105, C:S.175, C:S.175, C:G.422, C:E.508 ADP.11: 18 residues within 4Å: Chain D: L.43, P.45, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, K.170, G.410, M.480, I.493, E.495, K.500 Ligands: AF3.10, MG.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.99, D:T.99, D:T.100, D:S.101, D:S.101, D:S.168, D:S.168, D:S.169, D:G.410, D:E.495, D:K.500 Salt bridges: D:K.170 ADP.14: 17 residues within 4Å: Chain E: L.52, G.53, P.54, D.104, G.105, T.106, T.107, S.108, N.172, S.173, G.424, G.425, L.465, V.508, Q.510 Ligands: MG.13, AF3.15 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.53, E:G.105, E:T.106, E:T.107, E:S.108, E:N.172, E:S.173, E:S.173, E:G.425, E:Q.510 ADP.18: 18 residues within 4Å: Chain F: L.36, G.37, P.38, D.88, G.89, T.90, T.91, S.92, T.154, S.157, S.158, G.412, L.452, R.496, V.503, E.505 Ligands: AF3.16, MG.17 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.89, F:T.90, F:T.91, F:S.92, F:S.157, F:S.157, F:S.158, F:G.412, F:R.496, F:E.505, F:K.510 ADP.20: 18 residues within 4Å: Chain G: L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, G.410, G.411, L.451, I.495, E.497, K.502 Ligands: MG.19, AF3.21 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.42, G:G.94, G:T.95, G:T.96, G:S.97, G:S.97, G:T.162, G:G.411, G:K.502 ADP.23: 15 residues within 4Å: Chain H: N.37, L.38, G.39, P.40, D.90, G.91, S.94, T.158, G.410, A.411, L.451, V.494, D.496 Ligands: AF3.22, MG.24 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:G.39, H:S.94, H:S.94, H:T.158, H:A.411, H:D.496 ADP.26: 17 residues within 4Å: Chain I: Y.47, P.49, D.99, G.100, T.101, N.102, F.103, T.166, M.169, S.170, K.171, G.412, I.482, I.497, K.504 Ligands: AF3.25, MG.27 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:Y.47, I:T.101, I:F.103, I:G.412 Salt bridges: I:K.171, I:K.504 ADP.29: 16 residues within 4Å: Chain J: L.40, P.42, D.92, G.93, T.94, T.95, S.96, S.164, S.165, K.166, G.409, L.449, V.502, E.504 Ligands: MG.28, AF3.30 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:T.94, J:T.95, J:T.95, J:T.95, J:S.164, J:S.164, J:S.165, J:G.409, J:E.504, J:R.509 Salt bridges: J:K.166 ADP.31: 16 residues within 4Å: Chain K: S.51, L.52, G.53, P.54, G.105, T.106, T.107, T.171, T.172, S.175, G.422, L.462, V.506, E.508 Ligands: MG.32, AF3.33 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:G.53, K:G.105, K:T.106, K:S.175, K:G.422, K:E.508 ADP.34: 16 residues within 4Å: Chain L: L.43, P.45, D.97, G.98, T.99, T.100, S.101, S.168, S.169, G.410, I.450, M.480, I.493, E.495 Ligands: AF3.35, MG.36 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:T.99, L:T.100, L:S.101, L:S.168, L:S.168, L:S.169, L:G.410, L:E.495, L:K.500, L:K.500 Salt bridges: L:K.170, L:K.170 ADP.38: 16 residues within 4Å: Chain M: L.52, G.53, P.54, D.104, G.105, T.106, T.107, S.108, S.173, G.425, L.465, I.493, V.508, Q.510 Ligands: AF3.37, MG.39 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:G.53, M:G.105, M:T.106, M:T.107, M:T.107, M:T.107, M:N.172, M:S.173, M:S.173, M:G.425, M:Q.510 ADP.40: 16 residues within 4Å: Chain N: L.36, G.37, P.38, D.88, G.89, T.90, S.92, S.157, S.158, G.412, L.452, L.488, V.503, E.505 Ligands: AF3.41, MG.42 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:S.35, N:G.37, N:G.89, N:T.90, N:S.92, N:S.157, N:S.157, N:S.158, N:G.412, N:E.505 ADP.45: 16 residues within 4Å: Chain O: L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, G.411, L.451, I.495, E.497 Ligands: MG.43, AF3.44 7 PLIP interactions: 7 interactions with chain O Hydrogen bonds: O:G.42, O:G.94, O:T.95, O:S.97, O:S.97, O:G.411, O:E.497 ADP.48: 16 residues within 4Å: Chain P: N.37, L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.158, G.410, A.411, V.494, D.496 Ligands: AF3.46, MG.47 8 PLIP interactions: 8 interactions with chain P Hydrogen bonds: P:N.37, P:G.39, P:T.92, P:S.94, P:S.94, P:S.94, P:A.411, P:D.496

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 7 residues within 4Å: Chain A: D.68, D.99, T.101, K.171, D.394 Ligands: MG.1, ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.68 AF3.6: 7 residues within 4Å: Chain B: D.61, G.62, D.92, T.94, K.166 Ligands: MG.4, ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.61 AF3.7: 10 residues within 4Å: Chain C: N.72, D.73, D.104, G.105, T.106, T.107, K.176, D.404 Ligands: MG.8, ADP.9 No protein-ligand interaction detected (PLIP) AF3.10: 7 residues within 4Å: Chain D: D.66, D.97, T.99, K.170, D.392 Ligands: ADP.11, MG.12 No protein-ligand interaction detected (PLIP) AF3.15: 7 residues within 4Å: Chain E: D.73, D.104, G.105, T.106, K.174 Ligands: MG.13, ADP.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.73 AF3.16: 8 residues within 4Å: Chain F: D.57, G.87, D.88, G.89, T.90, K.159 Ligands: MG.17, ADP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.57 AF3.21: 8 residues within 4Å: Chain G: D.62, G.63, D.93, G.94, T.95, K.163 Ligands: MG.19, ADP.20 No protein-ligand interaction detected (PLIP) AF3.22: 9 residues within 4Å: Chain H: D.59, G.60, D.90, G.91, T.92, T.93, K.159 Ligands: ADP.23, MG.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.59, H:D.90 AF3.25: 9 residues within 4Å: Chain I: D.68, A.69, D.99, G.100, T.101, N.102, K.171 Ligands: ADP.26, MG.27 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.68 AF3.30: 7 residues within 4Å: Chain J: D.61, G.62, D.92, T.94, K.166 Ligands: MG.28, ADP.29 No protein-ligand interaction detected (PLIP) AF3.33: 10 residues within 4Å: Chain K: N.72, D.73, G.103, D.104, G.105, T.106, K.176, D.404 Ligands: ADP.31, MG.32 No protein-ligand interaction detected (PLIP) AF3.35: 8 residues within 4Å: Chain L: D.66, G.67, D.97, T.99, K.170, D.392 Ligands: ADP.34, MG.36 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.66 AF3.37: 9 residues within 4Å: Chain M: N.72, D.73, G.74, D.104, T.106, T.107, D.407 Ligands: ADP.38, MG.39 No protein-ligand interaction detected (PLIP) AF3.41: 9 residues within 4Å: Chain N: N.56, D.57, D.88, G.89, T.90, K.159, D.394 Ligands: ADP.40, MG.42 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.57 AF3.44: 7 residues within 4Å: Chain O: D.62, G.63, D.93, T.95, K.163 Ligands: MG.43, ADP.45 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.62 AF3.46: 9 residues within 4Å: Chain P: D.59, G.60, D.90, G.91, T.92, T.93, K.159 Ligands: MG.47, ADP.48 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.59, P:D.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Visualizing dynamic tubulin folding in chaperonin TRiC from nonnative nucleus to final native state. Nat Commun (2025)

Release Date

2025-10-08

Peptides

T-complex protein 1 subunit theta: AI
T-complex protein 1 subunit eta: BJ
T-complex protein 1 subunit epsilon: CK
T-complex protein 1 subunit beta: DL
T-complex protein 1 subunit delta: EM
T-complex protein 1 subunit alpha: FN
T-complex protein 1 subunit gamma: GO
T-complex protein 1 subunit zeta: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

I
b

B
C

J
c

C
D

K
d

D
E

L
e

E
F

M
f

F
G

N
g

G
H

O
h

H
I

P
i

T-complex protein 1 subunit theta

T-complex protein 1 subunit eta

T-complex protein 1 subunit epsilon

T-complex protein 1 subunit beta

T-complex protein 1 subunit delta

T-complex protein 1 subunit alpha

T-complex protein 1 subunit gamma

T-complex protein 1 subunit zeta

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