SMTL ID : 7nvo.1

Human TRiC complex in open state with nanobody bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

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

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

ADP.2: 18 residues within 4Å: Chain A: S.51, L.52, P.54, N.72, D.73, D.104, G.105, T.106, T.107, G.421, G.422, L.462, I.491, C.493, L.494, V.506, E.508 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.73, A:T.106, A:T.107, A:G.108, A:E.508 ADP.3: 16 residues within 4Å: Chain B: L.40, G.41, P.42, D.92, G.93, T.94, T.95, G.408, G.409, L.449, V.477, I.479, V.492, E.494 Ligands: MG.4, AF3.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.41, B:G.93, B:T.94, B:G.409, B:E.494 Water bridges: B:G.41, B:D.61 ADP.6: 17 residues within 4Å: Chain C: Y.47, P.49, D.99, G.100, T.101, N.102, F.103, T.166, M.169, S.170, G.412, L.452, I.482, I.497, D.499 Ligands: MG.7, AF3.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.100, C:T.101, C:N.102, C:F.103, C:T.166, C:S.170, C:G.412, C:D.499 ADP.9: 21 residues within 4Å: Chain D: N.37, L.38, G.39, P.40, K.58, D.90, T.92, T.93, S.94, T.154, T.158, G.410, A.411, G.412, L.451, V.479, L.481, D.496, K.501 Ligands: MG.10, AF3.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.37, D:G.39, D:A.411, D:G.412, D:D.496, D:K.501 Salt bridges: D:K.58 ADP.12: 17 residues within 4Å: Chain E: L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, G.410, G.411, L.451, V.480, G.482, I.495, E.497 Ligands: MG.13, AF3.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.42, E:G.94, E:T.95, E:T.96, E:S.97, E:G.411, E:G.482, E:E.497 ADP.15: 18 residues within 4Å: Chain F: L.36, G.37, P.38, D.88, G.89, T.90, T.91, S.92, G.411, G.412, L.452, L.488, L.490, V.503, E.505, K.510 Ligands: MG.16, AF3.17 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.88, F:G.89, F:T.90, F:S.92, F:G.412, F:E.505, F:K.510 ADP.19: 16 residues within 4Å: Chain G: S.51, L.52, G.53, P.54, D.73, G.74, D.104, T.106, T.107, G.425, I.461, L.465, I.493, V.495, V.508 Ligands: MG.18 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:G.53, G:G.74, G:T.106, G:G.425 ADP.20: 17 residues within 4Å: Chain H: L.43, G.44, P.45, D.97, G.98, T.99, T.100, S.101, T.165, G.409, G.410, I.450, M.480, I.493, E.495 Ligands: MG.21, AF3.22 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:G.98, H:T.99, H:T.100, H:S.101, H:S.101, H:S.101, H:S.101, H:G.410, H:E.495 ADP.24: 18 residues within 4Å: Chain J: S.51, L.52, P.54, N.72, D.73, D.104, G.105, T.106, T.107, G.421, G.422, L.462, I.491, C.493, L.494, V.506, E.508 Ligands: MG.23 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:D.73, J:T.106, J:T.107, J:G.108, J:E.508 ADP.25: 16 residues within 4Å: Chain K: L.40, G.41, P.42, D.92, G.93, T.94, T.95, G.408, G.409, L.449, V.477, I.479, V.492, E.494 Ligands: MG.26, AF3.27 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:G.41, K:G.93, K:T.94, K:G.409, K:E.494 Water bridges: K:G.41, K:D.61 ADP.28: 17 residues within 4Å: Chain L: Y.47, P.49, D.99, G.100, T.101, N.102, F.103, T.166, M.169, S.170, G.412, L.452, I.482, I.497, D.499 Ligands: MG.29, AF3.30 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:G.100, L:T.101, L:N.102, L:F.103, L:T.166, L:S.170, L:G.412, L:K.504, L:K.504 ADP.31: 21 residues within 4Å: Chain M: N.37, L.38, G.39, P.40, K.58, D.90, T.92, T.93, S.94, T.154, T.158, G.410, A.411, G.412, L.451, V.479, L.481, D.496, K.501 Ligands: MG.32, AF3.33 7 PLIP interactions: 7 interactions with chain M Hydrogen bonds: M:N.37, M:G.39, M:A.411, M:G.412, M:D.496, M:K.501 Salt bridges: M:K.58 ADP.34: 18 residues within 4Å: Chain N: L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, G.410, G.411, I.447, L.451, V.480, G.482, I.495, E.497 Ligands: MG.35, AF3.36 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:G.42, N:G.94, N:T.95, N:T.96, N:S.97, N:S.97, N:G.411, N:G.482, N:E.497 ADP.37: 18 residues within 4Å: Chain O: L.36, G.37, P.38, D.88, G.89, T.90, T.91, S.92, G.411, G.412, L.452, L.488, L.490, V.503, E.505, K.510 Ligands: MG.38, AF3.39 6 PLIP interactions: 6 interactions with chain O Hydrogen bonds: O:G.89, O:T.90, O:S.92, O:G.412, O:E.505, O:K.510 ADP.41: 16 residues within 4Å: Chain P: S.51, L.52, G.53, P.54, D.73, G.74, D.104, T.106, T.107, G.425, I.461, L.465, I.493, V.495, V.508 Ligands: MG.40 4 PLIP interactions: 4 interactions with chain P Hydrogen bonds: P:G.53, P:G.74, P:T.106, P:G.425 ADP.42: 17 residues within 4Å: Chain Q: L.43, G.44, P.45, D.97, G.98, T.99, T.100, S.101, T.165, G.409, G.410, I.450, M.480, I.493, E.495 Ligands: MG.43, AF3.44 9 PLIP interactions: 9 interactions with chain Q Hydrogen bonds: Q:G.98, Q:T.99, Q:T.100, Q:S.101, Q:S.101, Q:S.101, Q:S.101, Q:G.410, Q:E.495

12 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.5: 7 residues within 4Å: Chain B: D.61, D.92, G.93, T.94, T.95 Ligands: ADP.3, MG.4 No protein-ligand interaction detected (PLIP) AF3.8: 8 residues within 4Å: Chain C: D.68, A.70, D.99, T.101, N.102, D.394 Ligands: ADP.6, MG.7 No protein-ligand interaction detected (PLIP) AF3.11: 9 residues within 4Å: Chain D: D.59, G.60, N.61, D.90, T.92, T.93, K.159 Ligands: ADP.9, MG.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.90, D:D.90 AF3.14: 5 residues within 4Å: Chain E: D.93, T.95, T.96 Ligands: ADP.12, MG.13 No protein-ligand interaction detected (PLIP) AF3.17: 9 residues within 4Å: Chain F: D.57, G.58, A.59, D.88, G.89, T.90, T.91 Ligands: ADP.15, MG.16 No protein-ligand interaction detected (PLIP) AF3.22: 6 residues within 4Å: Chain H: D.66, D.97, T.99, T.100 Ligands: ADP.20, MG.21 No protein-ligand interaction detected (PLIP) AF3.27: 7 residues within 4Å: Chain K: D.61, D.92, G.93, T.94, T.95 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.30: 8 residues within 4Å: Chain L: D.68, A.70, D.99, T.101, N.102, D.394 Ligands: ADP.28, MG.29 No protein-ligand interaction detected (PLIP) AF3.33: 9 residues within 4Å: Chain M: D.59, G.60, N.61, D.90, T.92, T.93, K.159 Ligands: ADP.31, MG.32 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.90, M:D.90 AF3.36: 5 residues within 4Å: Chain N: D.93, T.95, T.96 Ligands: ADP.34, MG.35 No protein-ligand interaction detected (PLIP) AF3.39: 9 residues within 4Å: Chain O: D.57, G.58, A.59, D.88, G.89, T.90, T.91 Ligands: ADP.37, MG.38 No protein-ligand interaction detected (PLIP) AF3.44: 6 residues within 4Å: Chain Q: D.66, D.97, T.99, T.100 Ligands: ADP.42, MG.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kelly, J.J. et al., Snapshots of actin and tubulin folding inside the TRiC chaperonin. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-03-02

Peptides

T-complex protein 1 subunit epsilon: AJ
T-complex protein 1 subunit eta: BK
T-complex protein 1 subunit theta: CL
T-complex protein 1 subunit zeta: DM
T-complex protein 1 subunit gamma: EN
T-complex protein 1 subunit alpha: FO
T-complex protein 1 subunit delta: GP
T-complex protein 1 subunit beta: HQ
Nanobody: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

J
e

B
H

K
h

C
Q

L
q

D
Z

M
z

E
G

N
g

F
A

O
a

G
D

P
d

H
B

Q
b

I
N

R
n

T-complex protein 1 subunit epsilon

T-complex protein 1 subunit eta

T-complex protein 1 subunit theta

T-complex protein 1 subunit zeta

T-complex protein 1 subunit gamma

T-complex protein 1 subunit alpha

T-complex protein 1 subunit delta

T-complex protein 1 subunit beta

Nanobody

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