SMTL ID : 6ks6.1

TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1

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)

ADP.1: 19 residues within 4Å: Chain A: L.44, G.45, P.46, D.96, G.97, T.98, T.99, T.162, S.163, S.165, S.166, G.421, G.422, G.423, L.502, V.517, E.519 Ligands: MG.2, AF3.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.97, A:T.99, A:T.99, A:T.99, A:T.99, A:S.100, A:S.165, A:S.165, A:S.166, A:G.422, A:G.423 ADP.4: 17 residues within 4Å: Chain B: L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.162, S.165, S.166, G.421, G.422, V.517, E.519 Ligands: MG.5, AF3.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.45, B:G.97, B:T.98, B:T.99, B:T.99, B:S.100, B:S.165, B:S.165, B:S.166, B:S.166, B:G.422, B:G.423, B:E.519 Salt bridges: B:K.167, B:K.167 ADP.7: 21 residues within 4Å: Chain C: L.37, G.38, P.39, D.90, G.91, T.92, T.93, S.94, T.159, S.162, S.163, G.403, G.404, G.405, E.408, L.444, I.487, E.489, K.494 Ligands: MG.8, AF3.9 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.91, C:T.93, C:T.93, C:T.93, C:S.94, C:S.162, C:S.163, C:G.404, C:G.405, C:E.489, C:K.494 ADP.10: 21 residues within 4Å: Chain D: T.36, L.37, G.38, P.39, D.90, G.91, T.92, T.93, S.94, T.159, S.162, S.163, G.403, G.404, L.444, L.472, L.474, I.487, E.489 Ligands: MG.11, AF3.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.38, D:G.91, D:G.91, D:T.93, D:S.94, D:S.162, D:S.163, D:G.404, D:L.474, D:E.489 ADP.13: 22 residues within 4Å: Chain E: L.39, G.40, P.41, D.91, G.92, T.93, T.94, S.95, T.156, S.157, L.158, S.159, S.160, G.413, G.414, I.482, V.484, R.485, I.497, Q.499 Ligands: MG.14, AF3.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.40, E:D.91, E:G.92, E:G.92, E:T.94, E:S.95, E:S.159, E:G.414, E:V.484, E:R.485, E:Q.499 ADP.16: 19 residues within 4Å: Chain F: L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.156, S.157, S.159, S.160, K.161, G.414, L.454, I.482, V.484, I.497 Ligands: MG.17, AF3.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.40, F:G.92, F:T.93, F:T.94, F:S.159, F:S.159, F:S.160, F:G.414, F:G.415, F:V.484, F:Q.499 Salt bridges: F:K.161 ADP.19: 19 residues within 4Å: Chain G: L.65, G.66, P.67, D.117, G.118, T.119, T.120, T.186, S.187, S.190, G.442, G.443, L.483, M.522, V.527, D.529, K.534 Ligands: MG.20, AF3.21 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.66, G:G.118, G:T.119, G:T.120, G:T.120, G:S.190, G:S.190, G:G.443, G:D.529, G:K.534 ADP.22: 18 residues within 4Å: Chain H: L.65, G.66, P.67, D.117, G.118, T.119, T.120, T.186, G.189, S.190, G.442, G.443, L.515, V.527, D.529, K.534 Ligands: MG.23, AF3.24 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.66, H:G.118, H:T.119, H:T.120, H:S.190, H:S.190, H:G.443, H:G.444, H:D.529, H:K.534 ADP.25: 21 residues within 4Å: Chain I: L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, S.158, T.161, G.475, G.476, L.516, I.544, D.545, G.546, Y.557, I.559, E.561 Ligands: MG.26, AF3.27 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:G.40, I:G.92, I:T.94, I:T.95, I:T.95, I:G.476, I:D.545, I:G.546, I:E.561 ADP.28: 22 residues within 4Å: Chain J: L.39, P.41, D.91, G.92, T.93, T.94, T.95, A.157, S.158, T.161, K.162, G.475, G.476, G.477, L.516, I.544, G.546, Y.557, E.561, K.566 Ligands: MG.29, AF3.30 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:D.91, J:G.92, J:T.93, J:T.94, J:T.94, J:T.94, J:T.94, J:T.95, J:T.161, J:G.476, J:G.477, J:G.546, J:Y.557, J:K.566, J:K.566 Salt bridges: J:K.162 ADP.31: 18 residues within 4Å: Chain K: L.44, G.45, P.46, D.96, G.97, T.98, T.99, T.164, S.167, S.168, G.412, G.413, L.453, F.483, V.496, E.498 Ligands: MG.32, AF3.33 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:G.45, K:G.97, K:T.98, K:T.99, K:A.165, K:S.167, K:S.168, K:G.413, K:E.498 ADP.34: 19 residues within 4Å: Chain L: L.44, D.96, G.97, T.98, T.99, S.100, T.164, A.165, S.167, S.168, G.412, G.413, L.453, F.483, V.496, E.498, K.503 Ligands: MG.35, AF3.36 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.97, L:T.99, L:T.99, L:T.99, L:S.100, L:S.167, L:S.168, L:S.168, L:G.413, L:E.498, L:K.503 ADP.37: 17 residues within 4Å: Chain M: M.46, G.47, P.48, D.98, G.99, N.101, L.102, S.168, S.169, K.170, Y.172, G.422, A.423, L.463, I.517, D.519 Ligands: MG.38 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.99, M:N.101, M:L.102, M:S.169, M:Y.172, M:Y.172, M:A.423 Salt bridges: M:K.170, M:K.170, M:K.524 ADP.40: 16 residues within 4Å: Chain N: M.46, P.48, D.98, G.99, T.100, N.101, L.102, S.168, S.169, K.170, G.422, A.423, V.499, I.517, D.519 Ligands: MG.39 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:D.98, N:G.99, N:T.100, N:T.100, N:N.101, N:N.101, N:L.102, N:S.168, N:S.169, N:A.423, N:D.519 Salt bridges: N:K.170, N:K.170 ADP.41: 17 residues within 4Å: Chain O: L.37, P.39, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, L.458, V.491, I.506, D.508 Ligands: MG.42, AF3.43 10 PLIP interactions: 10 interactions with chain O Hydrogen bonds: O:G.90, O:T.91, O:T.92, O:T.92, O:T.93, O:T.160, O:T.160, O:A.415, O:G.416, O:D.508 ADP.44: 17 residues within 4Å: Chain P: L.37, P.39, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, L.458, V.491, I.506, D.508 Ligands: MG.45, AF3.46 8 PLIP interactions: 8 interactions with chain P Hydrogen bonds: P:G.90, P:T.92, P:T.92, P:T.92, P:T.93, P:A.415, P:G.416, P:D.508

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.96 Ligands: ADP.1, AF3.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.96, A:D.96 MG.5: 4 residues within 4Å: Chain B: D.96, K.167 Ligands: ADP.4, AF3.6 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: D.90, G.91, K.164 Ligands: ADP.7, AF3.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.90 MG.11: 4 residues within 4Å: Chain D: D.90, S.163 Ligands: ADP.10, AF3.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.90 MG.14: 3 residues within 4Å: Chain E: D.91, S.157 Ligands: ADP.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.91, E:S.157 MG.17: 3 residues within 4Å: Chain F: D.91, S.157 Ligands: ADP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.91, F:S.157 MG.20: 3 residues within 4Å: Chain G: D.117 Ligands: ADP.19, AF3.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.117 MG.23: 4 residues within 4Å: Chain H: D.117, S.187 Ligands: ADP.22, AF3.24 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.117 MG.26: 5 residues within 4Å: Chain I: D.91, G.92, S.158 Ligands: ADP.25, AF3.27 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.91 MG.29: 4 residues within 4Å: Chain J: D.91, S.158 Ligands: ADP.28, AF3.30 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.91 MG.32: 3 residues within 4Å: Chain K: D.96 Ligands: ADP.31, AF3.33 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.96 MG.35: 4 residues within 4Å: Chain L: D.96, A.165 Ligands: ADP.34, AF3.36 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.96 MG.38: 5 residues within 4Å: Chain M: D.98, V.166, S.169, K.170 Ligands: ADP.37 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain N: D.98, V.166, S.169 Ligands: ADP.40 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain O: D.89 Ligands: ADP.41, AF3.43 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.89, O:D.89 MG.45: 3 residues within 4Å: Chain P: D.89 Ligands: ADP.44, AF3.46 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.89, P:D.89

14 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 10 residues within 4Å: Chain A: D.65, G.95, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) AF3.6: 9 residues within 4Å: Chain B: N.64, D.65, G.66, T.98, T.99, K.167, D.404 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.9: 10 residues within 4Å: Chain C: N.58, D.59, D.90, G.91, T.92, T.93, K.164, D.386 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) AF3.12: 10 residues within 4Å: Chain D: D.59, G.60, D.90, T.92, T.93, S.163, K.164, D.386 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) AF3.15: 6 residues within 4Å: Chain E: D.60, T.93, T.94, K.161, D.396 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) AF3.18: 9 residues within 4Å: Chain F: N.59, D.60, G.61, H.62, T.93, T.94, K.161, D.396 Ligands: ADP.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.60 AF3.21: 9 residues within 4Å: Chain G: D.86, G.87, D.117, T.119, T.120, K.191, D.425 Ligands: ADP.19, MG.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 AF3.24: 7 residues within 4Å: Chain H: D.86, T.119, T.120, K.191, D.425 Ligands: ADP.22, MG.23 No protein-ligand interaction detected (PLIP) AF3.27: 10 residues within 4Å: Chain I: D.60, G.61, G.90, G.92, T.93, T.94, K.162, D.458 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.30: 10 residues within 4Å: Chain J: D.60, G.61, D.91, G.92, T.93, T.94, K.162, D.458 Ligands: ADP.28, MG.29 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.60 AF3.33: 8 residues within 4Å: Chain K: D.65, G.95, T.98, T.99, K.169, D.395 Ligands: ADP.31, MG.32 No protein-ligand interaction detected (PLIP) AF3.36: 9 residues within 4Å: Chain L: D.65, G.95, D.96, T.98, T.99, S.168, D.395 Ligands: ADP.34, MG.35 No protein-ligand interaction detected (PLIP) AF3.43: 11 residues within 4Å: Chain O: D.58, G.59, G.88, D.89, G.90, T.91, T.92, K.161, D.397 Ligands: ADP.41, MG.42 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.58 AF3.46: 7 residues within 4Å: Chain P: D.58, T.91, T.92, 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

Jin, M. et al., An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-18

Peptides

T-complex protein 1 subunit alpha: AB
T-complex protein 1 subunit beta: CD
T-complex protein 1 subunit delta: EF
T-complex protein 1 subunit epsilon: GH
fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma: IJ
T-complex protein 1 subunit eta: KL
T-complex protein 1 subunit theta: MN
T-complex protein 1 subunit zeta: OP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
A

C
b

D
B

E
d

F
D

G
e

H
E

I
g

J
G

K
h

L
H

M
q

N
Q

O
z

P
Z

T-complex protein 1 subunit alpha

T-complex protein 1 subunit beta

T-complex protein 1 subunit delta

T-complex protein 1 subunit epsilon

fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma

T-complex protein 1 subunit eta

T-complex protein 1 subunit theta

T-complex protein 1 subunit zeta

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