SMTL ID : 7x0v.1

cryo-EM structure of human TRiC-ADP-AlFx

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.154, T.158, G.410, A.411, L.451, L.481, V.494, D.496, K.501 Ligands: MG.2, AF3.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.39, A:D.90, A:D.90, A:G.91, A:G.91, A:T.92, A:T.93, A:T.93, A:S.94, A:S.94, A:S.94, A:G.410, A:K.501 Salt bridges: A:K.159, A:K.159 ADP.4: 18 residues within 4Å: Chain B: Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, M.169, S.170, G.412, G.413, L.452, L.480, I.482, I.497 Ligands: MG.5, AF3.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.47, B:G.100, B:T.101, B:T.101, B:N.102, B:N.102, B:F.103, B:G.412, B:G.413 Salt bridges: B:K.171, B:K.171 ADP.7: 19 residues within 4Å: Chain C: L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, S.164, S.165, G.408, G.409, L.449, V.477, I.479, V.492, R.499 Ligands: MG.8, AF3.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.41, C:T.95, C:S.96, C:S.164, C:S.165, C:G.409, C:G.409, C:R.499 ADP.10: 16 residues within 4Å: Chain D: L.41, D.93, G.94, T.95, T.96, S.97, T.162, G.410, G.411, L.451, V.480, G.482, I.495, E.497 Ligands: MG.11, AF3.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.92, D:T.95, D:T.96, D:S.97, D:S.97, D:S.97, D:T.162, D:G.411, D:G.482, D:E.497 ADP.13: 20 residues within 4Å: Chain E: L.50, G.51, P.52, D.102, G.103, T.104, T.105, G.106, T.169, S.173, G.419, G.420, G.421, I.489, D.490, K.494, V.504, E.506 Ligands: MG.14, AF3.15 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:T.104, E:T.105, E:T.105, E:G.106, E:S.173, E:G.420, E:G.421, E:D.490, E:E.506 ADP.16: 17 residues within 4Å: Chain F: G.53, P.54, D.73, D.104, G.105, T.106, T.107, S.108, T.169, N.172, G.425, G.426, L.465, I.493, V.508 Ligands: MG.17, AF3.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.105, F:T.106, F:T.106, F:T.106, F:T.107, F:S.108, F:S.108, F:S.108, F:N.172, F:G.425, F:G.426 Salt bridges: F:K.174 ADP.19: 21 residues within 4Å: Chain G: L.43, G.44, P.45, D.66, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, G.410, I.450, L.478, M.480, I.493, E.495, K.500 Ligands: MG.20, AF3.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.44, G:G.98, G:T.99, G:T.100, G:S.101, G:S.101, G:S.101, G:S.168, G:S.169, G:G.410, G:E.495, G:K.500 ADP.22: 20 residues within 4Å: Chain H: L.36, G.37, P.38, D.88, G.89, T.90, T.91, S.92, T.154, S.157, S.158, G.411, G.412, G.413, L.488, V.503, E.505, K.510 Ligands: MG.23, AF3.24 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.89, H:T.90, H:T.91, H:S.92, H:S.157, H:S.158, H:G.412, H:G.413, H:E.505, H:K.510 Salt bridges: H:K.159 ADP.25: 19 residues within 4Å: Chain I: L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.154, T.158, G.410, A.411, L.451, L.481, V.494, D.496, K.501 Ligands: MG.26, AF3.27 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.39, I:G.91, I:T.92, I:T.93, I:T.93, I:T.93, I:T.93, I:S.94, I:S.94, I:S.94, I:G.410, I:D.496, I:K.501 Salt bridges: I:K.159, I:K.159 ADP.28: 18 residues within 4Å: Chain J: Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, M.169, S.170, G.412, G.413, L.452, L.480, I.482, I.497 Ligands: MG.29, AF3.30 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:Y.47, J:Y.47, J:G.100, J:T.101, J:T.101, J:N.102, J:F.103, J:G.412, J:G.413 Salt bridges: J:K.171 ADP.33: 19 residues within 4Å: Chain K: L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, S.164, S.165, G.408, G.409, L.449, V.477, I.479, V.492, R.499 Ligands: MG.31, AF3.32 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:G.41, K:G.93, K:T.94, K:T.95, K:S.96, K:S.164, K:S.165, K:G.409, K:G.409, K:R.499 ADP.34: 17 residues within 4Å: Chain L: L.41, P.43, D.93, G.94, T.95, T.96, S.97, T.162, G.410, G.411, L.451, V.480, G.482, I.495, E.497 Ligands: MG.35, AF3.36 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:T.95, L:T.96, L:T.96, L:T.96, L:S.97, L:S.97, L:S.97, L:T.162, L:G.411, L:G.482, L:E.483, L:E.497, L:E.497 ADP.37: 20 residues within 4Å: Chain M: L.50, G.51, P.52, D.71, D.102, G.103, T.104, T.105, G.106, T.169, S.173, G.419, G.420, G.421, I.489, D.490, V.504, E.506 Ligands: MG.38, AF3.39 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:T.104, M:T.104, M:T.105, M:T.105, M:T.105, M:G.106, M:S.173, M:G.420, M:G.421, M:D.490, M:E.506 ADP.40: 18 residues within 4Å: Chain N: 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.488, V.503, E.505, K.510 Ligands: MG.41, AF3.42 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:D.88, N:G.89, N:T.90, N:T.91, N:T.91, N:T.91, N:S.92, N:S.157, N:S.158, N:G.412, N:G.413, N:E.505, N:K.510 Salt bridges: N:K.159 ADP.43: 17 residues within 4Å: Chain O: G.53, P.54, D.73, D.104, G.105, T.106, T.107, S.108, T.169, N.172, G.425, G.426, L.465, I.493, V.508 Ligands: MG.44, AF3.45 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:G.105, O:T.106, O:T.106, O:T.107, O:T.107, O:T.107, O:S.108, O:N.172, O:G.425, O:G.426 Salt bridges: O:K.174 ADP.46: 21 residues within 4Å: Chain P: L.43, G.44, P.45, D.66, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, G.410, I.450, L.478, M.480, I.493, E.495, K.500 Ligands: MG.47, AF3.48 16 PLIP interactions: 16 interactions with chain P Hydrogen bonds: P:G.44, P:D.66, P:G.98, P:T.99, P:T.99, P:T.100, P:T.100, P:T.100, P:S.101, P:S.101, P:S.101, P:S.168, P:S.169, P:G.410, P:E.495, P:K.500

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.90, G.91, D.393 Ligands: ADP.1, AF3.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.90, A:D.90 MG.5: 5 residues within 4Å: Chain B: D.99, S.170, K.171 Ligands: ADP.4, AF3.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.170 MG.8: 4 residues within 4Å: Chain C: D.92, A.162 Ligands: ADP.7, AF3.9 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain D: D.93, S.159, K.163 Ligands: ADP.10, AF3.12 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain E: T.170, S.173 Ligands: ADP.13, AF3.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.173 MG.17: 5 residues within 4Å: Chain F: D.104, S.170, S.173 Ligands: ADP.16, AF3.18 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain G: D.97, T.166, S.169 Ligands: ADP.19, AF3.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.97, G:D.97 MG.23: 6 residues within 4Å: Chain H: D.88, S.155, S.158, K.159 Ligands: ADP.22, AF3.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.88, H:D.88 MG.26: 5 residues within 4Å: Chain I: D.90, G.91, K.159 Ligands: ADP.25, AF3.27 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.90, I:D.90 MG.29: 5 residues within 4Å: Chain J: D.99, S.170, K.171 Ligands: ADP.28, AF3.30 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.170 MG.31: 3 residues within 4Å: Chain K: D.92 Ligands: AF3.32, ADP.33 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.92, K:D.92 MG.35: 6 residues within 4Å: Chain L: D.93, S.159, T.162, K.163 Ligands: ADP.34, AF3.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.93, L:D.93 MG.38: 4 residues within 4Å: Chain M: T.170, S.173 Ligands: ADP.37, AF3.39 No protein-ligand interaction detected (PLIP) MG.41: 5 residues within 4Å: Chain N: S.155, S.158, K.159 Ligands: ADP.40, AF3.42 No protein-ligand interaction detected (PLIP) MG.44: 5 residues within 4Å: Chain O: D.104, S.170, S.173 Ligands: ADP.43, AF3.45 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.104 MG.47: 5 residues within 4Å: Chain P: D.97, T.166, S.169 Ligands: ADP.46, AF3.48 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.97, P:D.97

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

AF3.3: 11 residues within 4Å: Chain A: D.59, G.60, D.85, G.89, D.90, T.92, T.93, K.159, D.393 Ligands: ADP.1, MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.59, A:D.90 AF3.6: 9 residues within 4Å: Chain B: D.68, A.69, D.99, T.101, N.102, K.171, D.394 Ligands: ADP.4, MG.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.68 AF3.9: 10 residues within 4Å: Chain C: D.61, G.62, G.91, D.92, T.94, T.95, K.166, D.391 Ligands: ADP.7, MG.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.61, C:D.92, C:T.94 AF3.12: 11 residues within 4Å: Chain D: D.62, G.63, N.64, G.92, D.93, T.95, T.96, K.163, D.393 Ligands: ADP.10, MG.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.62, D:T.95 AF3.15: 9 residues within 4Å: Chain E: D.71, G.72, D.102, T.104, T.105, K.174, D.402 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) AF3.18: 9 residues within 4Å: Chain F: D.73, G.74, G.103, T.106, T.107, K.174, D.407 Ligands: ADP.16, MG.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.73 AF3.21: 10 residues within 4Å: Chain G: N.65, D.66, G.67, D.97, T.99, T.100, K.170, D.392 Ligands: ADP.19, MG.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.66 AF3.24: 10 residues within 4Å: Chain H: D.57, G.58, D.88, T.90, T.91, S.158, K.159, D.394 Ligands: ADP.22, MG.23 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.57 AF3.27: 12 residues within 4Å: Chain I: D.59, G.60, D.85, G.89, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.25, MG.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.59, I:D.90 AF3.30: 9 residues within 4Å: Chain J: D.68, A.69, D.99, T.101, N.102, K.171, D.394 Ligands: ADP.28, MG.29 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.68 AF3.32: 11 residues within 4Å: Chain K: D.61, G.62, G.91, D.92, G.93, T.94, T.95, K.166, D.391 Ligands: MG.31, ADP.33 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.61 AF3.36: 11 residues within 4Å: Chain L: D.62, G.63, N.64, G.92, D.93, T.95, T.96, K.163, D.393 Ligands: ADP.34, MG.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.62, L:D.93 AF3.39: 10 residues within 4Å: Chain M: D.71, G.72, D.102, T.104, T.105, S.173, K.174, D.402 Ligands: ADP.37, MG.38 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.71 AF3.42: 10 residues within 4Å: Chain N: D.57, G.58, D.88, T.90, T.91, S.158, K.159, D.394 Ligands: ADP.40, MG.41 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.57 AF3.45: 10 residues within 4Å: Chain O: D.73, G.74, G.103, D.104, T.106, T.107, K.174, D.407 Ligands: ADP.43, MG.44 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.73 AF3.48: 10 residues within 4Å: Chain P: N.65, D.66, G.67, D.97, T.99, T.100, K.170, D.392 Ligands: ADP.46, MG.47 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. Commun Biol (2023)

Release Date

2023-04-12

Peptides

T-complex protein 1 subunit zeta: AI
T-complex protein 1 subunit theta: BJ
T-complex protein 1 subunit eta: CK
T-complex protein 1 subunit gamma: DL
T-complex protein 1 subunit epsilon: EM
T-complex protein 1 subunit delta: FO
T-complex protein 1 subunit beta: GP
T-complex protein 1 subunit alpha: HN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

I
z

B
J

J
P

C
H

K
O

D
G

L
N

E
E

M
e

F
I

O
M

G
B

P
L

H
A

N
a

T-complex protein 1 subunit zeta

T-complex protein 1 subunit theta

T-complex protein 1 subunit eta

T-complex protein 1 subunit gamma

T-complex protein 1 subunit epsilon

T-complex protein 1 subunit delta

T-complex protein 1 subunit beta

T-complex protein 1 subunit alpha

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