SMTL ID : 7nvm.1

Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: S.35, 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, L.452, L.488, R.496, V.503, E.505, K.510 Ligands: MG.2, AF3.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.37, A:G.89, A:T.90, A:T.91, A:T.91, A:T.91, A:S.92, A:S.92, A:S.92, A:S.157, A:S.157, A:S.158, A:S.158, A:G.412, A:G.413, A:R.496, A:E.505, A:K.510 Salt bridges: A:K.159 ADP.4: 20 residues within 4Å: Chain B: T.42, L.43, G.44, P.45, N.65, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, G.410, L.478, M.480, I.493, E.495 Ligands: MG.5, AF3.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.44, B:N.65, B:G.98, B:G.98, B:T.99, B:T.99, B:T.100, B:T.100, B:S.101, B:S.168, B:S.169, B:G.410, B:M.480, B:E.495 Water bridges: B:T.42 ADP.7: 23 residues within 4Å: Chain C: S.51, L.52, G.53, P.54, D.104, G.105, T.106, T.107, S.108, T.169, N.172, S.173, K.174, G.424, G.425, G.426, L.465, I.493, V.495, V.508, Q.510 Ligands: MG.8, AF3.9 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.51, C:G.53, C:D.104, C:G.105, C:T.106, C:T.107, C:T.107, C:S.108, C:N.172, C:S.173, C:G.425, C:G.426, C:Q.510 Salt bridges: C:K.174, C:K.174 ADP.10: 27 residues within 4Å: Chain D: S.51, L.52, G.53, P.54, N.72, D.104, G.105, T.106, T.107, G.108, T.171, T.172, S.175, G.421, G.422, G.423, E.426, L.462, I.491, C.493, L.494, M.501, V.506, E.508, Q.516 Ligands: MG.11, AF3.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.53, D:N.72, D:G.105, D:T.106, D:T.106, D:T.107, D:T.107, D:G.108, D:S.175, D:G.422, D:G.423, D:E.508, D:Q.516 Salt bridges: D:K.176 ADP.13: 23 residues within 4Å: Chain E: C.40, L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, K.163, G.410, G.411, L.451, V.480, N.481, G.482, E.483, I.495, E.497 Ligands: MG.14, AF3.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.42, E:D.93, E:G.94, E:G.94, E:T.95, E:T.96, E:S.97, E:T.161, E:T.162, E:G.411, E:G.482, E:E.483, E:E.497 Salt bridges: E:K.163 ADP.16: 22 residues within 4Å: Chain F: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, T.161, S.164, S.165, G.408, G.409, I.445, L.449, V.477, I.479, V.492, R.499 Ligands: MG.17, AF3.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.41, F:G.93, F:T.94, F:T.94, F:T.95, F:S.96, F:S.96, F:S.96, F:S.164, F:S.164, F:S.165, F:S.165, F:G.409, F:R.499 Salt bridges: F:K.166 ADP.19: 21 residues within 4Å: Chain H: A.46, Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, T.166, M.169, S.170, K.171, G.411, G.412, L.452, I.482, I.497, D.499 Ligands: MG.20, AF3.21 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:Y.47, H:G.48, H:G.100, H:G.100, H:T.101, H:N.102, H:F.103, H:S.170, H:G.412, H:D.499 Salt bridges: H:K.171 ADP.22: 22 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, K.159, G.410, A.411, I.447, L.451, V.479, L.481, V.494, D.496, K.501 Ligands: MG.23, AF3.24 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.39, I:G.91, I:G.91, I:T.93, I:T.93, I:T.93, I:S.94, I:A.411, I:D.496, I:K.501 Salt bridges: I:K.159, I:K.159 ADP.25: 21 residues within 4Å: Chain J: S.35, 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, L.452, L.488, V.503, E.505, K.510 Ligands: MG.26, AF3.27 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:G.37, J:G.89, J:T.90, J:T.91, J:T.91, J:T.91, J:S.92, J:S.157, J:S.157, J:S.158, J:S.158, J:G.412, J:G.413, J:R.496, J:E.505, J:K.510 Water bridges: J:G.58 ADP.28: 20 residues within 4Å: Chain K: T.42, L.43, G.44, P.45, N.65, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, G.410, L.478, M.480, I.493, E.495 Ligands: MG.29, AF3.30 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:G.44, K:N.65, K:G.98, K:G.98, K:T.99, K:T.99, K:T.100, K:T.100, K:S.101, K:S.168, K:S.169, K:G.410, K:M.480 ADP.31: 22 residues within 4Å: Chain L: S.51, L.52, G.53, P.54, G.105, T.106, T.107, S.108, T.169, N.172, S.173, K.174, G.424, G.425, G.426, E.429, L.465, I.493, V.508, Q.510 Ligands: MG.32, AF3.33 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:S.51, L:G.53, L:G.105, L:G.105, L:T.106, L:T.107, L:T.107, L:S.108, L:N.172, L:S.173, L:G.425, L:G.426, L:Q.510 Salt bridges: L:K.174, L:K.174 ADP.34: 24 residues within 4Å: Chain M: S.51, L.52, G.53, P.54, N.72, D.104, G.105, T.106, T.107, T.171, T.172, S.175, G.422, G.423, E.426, L.462, I.491, C.493, L.494, V.506, E.508, K.513 Ligands: MG.35, AF3.36 16 PLIP interactions: 16 interactions with chain M Hydrogen bonds: M:G.53, M:N.72, M:G.105, M:T.106, M:T.106, M:T.107, M:T.107, M:G.108, M:S.175, M:G.422, M:G.423, M:E.508, M:K.513, M:Q.516 Salt bridges: M:K.176, M:K.176 ADP.37: 23 residues within 4Å: Chain N: C.40, L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, K.163, G.410, G.411, L.451, V.480, N.481, G.482, I.495, E.497, K.502 Ligands: MG.38, AF3.39 16 PLIP interactions: 16 interactions with chain N Hydrogen bonds: N:G.42, N:D.93, N:G.94, N:G.94, N:T.95, N:T.96, N:T.96, N:S.97, N:T.161, N:T.162, N:G.411, N:G.482, N:E.497, N:K.502 Salt bridges: N:K.163, N:K.163 ADP.40: 22 residues within 4Å: Chain O: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, T.161, S.164, S.165, K.166, G.408, G.409, I.445, L.449, V.477, V.492, R.499 Ligands: MG.41, AF3.42 13 PLIP interactions: 13 interactions with chain O Hydrogen bonds: O:G.41, O:G.93, O:T.94, O:T.95, O:T.95, O:S.96, O:S.96, O:S.164, O:S.164, O:S.165, O:G.409, O:R.499 Salt bridges: O:K.166 ADP.43: 21 residues within 4Å: Chain Q: A.46, Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, M.169, S.170, K.171, G.411, G.412, L.452, L.480, I.482, I.497, D.499 Ligands: MG.44, AF3.45 12 PLIP interactions: 12 interactions with chain Q Hydrogen bonds: Q:Y.47, Q:G.48, Q:D.99, Q:G.100, Q:G.100, Q:T.101, Q:N.102, Q:F.103, Q:S.170, Q:G.412, Q:D.499 Salt bridges: Q:K.171 ADP.46: 22 residues within 4Å: Chain R: N.37, L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.154, T.158, K.159, G.410, A.411, L.451, V.479, L.481, V.494, D.496, K.501 Ligands: MG.47, AF3.48 12 PLIP interactions: 12 interactions with chain R Hydrogen bonds: R:G.39, R:G.91, R:G.91, R:T.93, R:T.93, R:T.93, R:S.94, R:A.411, R:D.496, R:K.501 Salt bridges: R:K.159, R:K.159

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.88, S.155 Ligands: ADP.1, AF3.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.88, A:D.88 MG.5: 5 residues within 4Å: Chain B: D.97, T.166, K.170 Ligands: ADP.4, AF3.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.97 MG.8: 5 residues within 4Å: Chain C: D.104, S.170, K.174 Ligands: ADP.7, AF3.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: D.104, T.172 Ligands: ADP.10, AF3.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.104, D:D.104 MG.14: 5 residues within 4Å: Chain E: D.93, S.159, T.162 Ligands: ADP.13, AF3.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.93, E:D.93 MG.17: 4 residues within 4Å: Chain F: D.92, A.162 Ligands: ADP.16, AF3.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.92, F:D.92 MG.20: 3 residues within 4Å: Chain H: D.99 Ligands: ADP.19, AF3.21 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.99, H:D.99 MG.23: 4 residues within 4Å: Chain I: D.90, T.158, K.159 Ligands: ADP.22 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.90, I:D.90 MG.26: 4 residues within 4Å: Chain J: D.88, S.155 Ligands: ADP.25, AF3.27 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.88, J:D.88 MG.29: 5 residues within 4Å: Chain K: D.97, T.166, K.170 Ligands: ADP.28, AF3.30 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.97, K:D.97 MG.32: 5 residues within 4Å: Chain L: D.104, S.170, K.174 Ligands: ADP.31, AF3.33 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain M: D.104, T.172, S.175 Ligands: ADP.34, AF3.36 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.104 MG.38: 6 residues within 4Å: Chain N: D.93, S.159, T.162, K.163 Ligands: ADP.37, AF3.39 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.93, N:D.93 MG.41: 4 residues within 4Å: Chain O: D.92, A.162 Ligands: ADP.40, AF3.42 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.92, O:D.92 MG.44: 2 residues within 4Å: Chain Q: D.99 Ligands: ADP.43 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.99, Q:D.99 MG.47: 4 residues within 4Å: Chain R: D.90, T.158, K.159 Ligands: ADP.46 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:D.90, R:D.90

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 11 residues within 4Å: Chain A: N.56, D.57, G.58, D.88, G.89, T.90, T.91, K.159, D.394 Ligands: ADP.1, MG.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.90 AF3.6: 11 residues within 4Å: Chain B: N.65, D.66, G.67, D.97, G.98, T.99, T.100, K.170, D.392 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.9: 11 residues within 4Å: Chain C: N.72, D.73, G.74, D.104, G.105, T.106, T.107, K.174, D.407 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) AF3.12: 9 residues within 4Å: Chain D: D.73, G.74, D.104, T.106, T.107, K.176, D.404 Ligands: ADP.10, MG.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.73 AF3.15: 11 residues within 4Å: Chain E: N.61, D.62, G.63, D.93, G.94, T.95, T.96, K.163, D.393 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) AF3.18: 11 residues within 4Å: Chain F: N.60, D.61, G.62, D.92, G.93, T.94, T.95, K.166, D.391 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP) AF3.21: 11 residues within 4Å: Chain H: N.67, D.68, A.69, D.99, G.100, T.101, N.102, K.171, D.394 Ligands: ADP.19, MG.20 No protein-ligand interaction detected (PLIP) AF3.24: 10 residues within 4Å: Chain I: D.59, G.60, G.89, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.22 No protein-ligand interaction detected (PLIP) AF3.27: 11 residues within 4Å: Chain J: N.56, D.57, G.58, D.88, G.89, T.90, T.91, K.159, D.394 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.30: 11 residues within 4Å: Chain K: N.65, D.66, G.67, G.96, D.97, T.99, T.100, K.170, D.392 Ligands: ADP.28, MG.29 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.66 AF3.33: 11 residues within 4Å: Chain L: D.73, G.74, G.103, D.104, G.105, T.106, T.107, K.174, D.407 Ligands: ADP.31, MG.32 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.73 AF3.36: 9 residues within 4Å: Chain M: D.73, G.74, D.104, T.106, T.107, K.176, D.404 Ligands: ADP.34, MG.35 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.73, M:T.106 AF3.39: 10 residues within 4Å: Chain N: N.61, D.62, G.63, D.93, G.94, T.95, T.96, K.163 Ligands: ADP.37, MG.38 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.95 AF3.42: 10 residues within 4Å: Chain O: D.61, G.62, D.92, G.93, T.94, T.95, K.166, D.391 Ligands: ADP.40, MG.41 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.94 AF3.45: 10 residues within 4Å: Chain Q: D.68, A.69, G.98, D.99, G.100, T.101, N.102, K.171, D.394 Ligands: ADP.43 No protein-ligand interaction detected (PLIP) AF3.48: 9 residues within 4Å: Chain R: D.59, G.60, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.46 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 alpha: AJ
T-complex protein 1 subunit beta: BK
T-complex protein 1 subunit delta: CL
T-complex protein 1 subunit epsilon: DM
T-complex protein 1 subunit gamma: EN
T-complex protein 1 subunit eta: FO
Nanobody Nb18: GP
T-complex protein 1 subunit theta: HQ
T-complex protein 1 subunit zeta: IR
Actin, cytoplasmic 2: S
Phosducin-like protein 3: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
a

B
B

K
b

C
D

L
d

D
E

M
e

E
G

N
g

F
H

O
h

G
N

P
n

H
Q

Q
q

I
Z

R
z

S
K

T
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

Nanobody Nb18

T-complex protein 1 subunit theta

T-complex protein 1 subunit zeta

Actin, cytoplasmic 2

Phosducin-like protein 3

Related Entries With Identical Sequence