SMTL ID : 4v94.1 (1 other biounit)

Molecular architecture of the eukaryotic chaperonin TRiC/CCT derived by a combination of chemical crosslinking and mass-spectrometry, XL-MS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.89, T.160, K.161 Ligands: ADP.2, BEF.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.89, A:D.89 MG.4: 4 residues within 4Å: Chain B: D.98, S.169 Ligands: ADP.5, BEF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.98 MG.7: 4 residues within 4Å: Chain C: D.96, K.169 Ligands: ADP.8, BEF.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.96 MG.10: 5 residues within 4Å: Chain D: D.117, S.187, K.191 Ligands: ADP.11, BEF.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.117, D:D.117 MG.13: 3 residues within 4Å: Chain E: D.90 Ligands: ADP.14, BEF.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.90, E:D.90 MG.16: 5 residues within 4Å: Chain F: D.91, S.157, K.161 Ligands: ADP.17, BEF.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.91 MG.19: 5 residues within 4Å: Chain G: D.96, S.163, K.167 Ligands: ADP.20, BEF.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.96, G:D.96 MG.22: 4 residues within 4Å: Chain H: D.91, T.161 Ligands: ADP.23, BEF.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.91, H:D.91 MG.25: 5 residues within 4Å: Chain I: D.89, T.160, K.161 Ligands: ADP.26, BEF.27 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.89, I:T.160 MG.28: 4 residues within 4Å: Chain J: D.98, S.169 Ligands: ADP.29, BEF.30 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.98 MG.31: 4 residues within 4Å: Chain K: D.96, K.169 Ligands: ADP.32, BEF.33 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.96 MG.34: 4 residues within 4Å: Chain L: D.117, S.187 Ligands: ADP.35, BEF.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.117, L:D.117 MG.37: 4 residues within 4Å: Chain M: D.90, T.160 Ligands: ADP.38, BEF.39 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain N: D.91, S.157, K.161 Ligands: ADP.41, BEF.42 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.91 MG.43: 5 residues within 4Å: Chain O: D.96, S.163, K.167 Ligands: ADP.44, BEF.45 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.96, O:D.96 MG.46: 4 residues within 4Å: Chain P: D.91, K.162 Ligands: ADP.47, BEF.48 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.91

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

ADP.2: 20 residues within 4Å: Chain A: N.36, L.37, G.38, P.39, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, I.454, L.458, V.491, L.493, I.506 Ligands: MG.1, BEF.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.38, A:G.90, A:T.91, A:T.92, A:T.92, A:T.93, A:T.93, A:T.93, A:A.415, A:G.416 Salt bridges: A:K.161 ADP.5: 19 residues within 4Å: Chain B: M.46, G.47, P.48, N.66, D.98, G.99, T.100, N.101, L.102, P.165, S.169, G.422, A.423, G.424, I.517, D.519, K.524 Ligands: MG.4, BEF.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.47, B:G.99, B:G.99, B:G.99, B:N.101, B:N.101, B:L.102, B:S.168, B:S.168, B:S.169, B:A.423, B:G.424, B:D.519, B:K.524 ADP.8: 22 residues within 4Å: Chain C: T.43, L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.164, S.167, S.168, G.412, G.413, G.414, L.453, V.481, V.496, E.498, K.503 Ligands: MG.7, BEF.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.45, C:G.97, C:G.97, C:G.97, C:T.99, C:S.100, C:S.167, C:S.167, C:S.168, C:G.413, C:G.414, C:E.498, C:K.503 Salt bridges: C:K.169 ADP.11: 22 residues within 4Å: Chain D: S.64, L.65, G.66, P.67, N.85, D.117, G.118, T.119, T.120, G.121, T.186, G.189, S.190, G.442, G.443, L.483, V.512, C.514, V.527, D.529 Ligands: MG.10, BEF.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.66, D:G.118, D:G.118, D:G.118, D:T.120, D:T.120, D:G.121, D:S.190, D:G.443, D:D.529 ADP.14: 25 residues within 4Å: Chain E: T.36, L.37, G.38, P.39, N.58, D.90, G.91, T.92, T.93, S.94, T.159, S.162, S.163, K.164, G.403, G.404, G.405, E.408, L.444, L.472, I.487, E.489, K.494 Ligands: MG.13, BEF.15 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:G.38, E:D.90, E:G.91, E:G.91, E:T.92, E:T.93, E:T.93, E:S.94, E:S.94, E:S.94, E:S.162, E:S.162, E:S.163, E:G.404, E:G.405, E:E.489, E:K.494 Salt bridges: E:K.164 ADP.17: 21 residues within 4Å: Chain F: S.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, S.95, T.156, S.160, G.413, G.414, L.454, I.482, V.484, I.497, Q.499 Ligands: MG.16, BEF.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.40, F:D.91, F:G.92, F:T.94, F:T.94, F:S.95, F:S.95, F:S.95, F:S.95, F:S.160, F:G.414, F:V.484, F:Q.499, F:Q.499 Salt bridges: F:K.161 ADP.20: 22 residues within 4Å: Chain G: S.43, 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, G.423, L.462, L.502, E.512, V.517, E.519 Ligands: MG.19, BEF.21 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:G.45, G:G.97, G:G.97, G:G.97, G:T.99, G:T.99, G:S.100, G:S.165, G:S.165, G:S.166, G:G.422, G:G.423, G:E.519, G:K.524 Salt bridges: G:K.167, G:K.167 ADP.23: 22 residues within 4Å: Chain H: C.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, G.160, T.161, G.471, G.472, I.540, D.541, G.542, Y.553, I.555, E.557 Ligands: MG.22, BEF.24 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:G.40, H:D.91, H:G.92, H:G.92, H:T.93, H:T.94, H:T.94, H:T.95, H:T.95, H:T.161, H:G.472, H:G.473, H:G.542, H:Y.553, H:Y.553, H:E.557, H:E.557 ADP.26: 21 residues within 4Å: Chain I: N.36, L.37, G.38, P.39, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, I.454, L.458, V.491, L.493, I.506, D.508 Ligands: MG.25, BEF.27 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.38, I:G.90, I:T.91, I:T.92, I:T.92, I:T.93, I:T.93, I:T.93, I:A.415, I:G.416, I:D.508, I:D.508 ADP.29: 21 residues within 4Å: Chain J: S.45, M.46, G.47, P.48, N.66, D.98, G.99, T.100, N.101, L.102, P.165, S.168, S.169, G.422, A.423, L.463, I.517, D.519, K.524 Ligands: MG.28, BEF.30 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.47, J:G.99, J:G.99, J:N.101, J:L.102, J:S.168, J:S.168, J:S.169, J:A.423, J:D.519, J:K.524 ADP.32: 22 residues within 4Å: Chain K: T.43, L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.164, S.167, S.168, G.412, G.413, G.414, L.453, V.481, V.496, E.498, K.503 Ligands: MG.31, BEF.33 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.45, K:G.97, K:G.97, K:G.97, K:T.99, K:T.99, K:S.100, K:S.167, K:S.167, K:S.168, K:G.413, K:G.414, K:E.498, K:K.503 Salt bridges: K:K.169 ADP.35: 23 residues within 4Å: Chain L: S.64, L.65, G.66, P.67, N.85, D.117, G.118, T.119, T.120, G.121, T.186, G.189, S.190, G.442, G.443, L.483, V.512, C.514, L.515, V.527, D.529 Ligands: MG.34, BEF.36 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.66, L:G.118, L:G.118, L:G.118, L:T.120, L:T.120, L:G.121, L:S.190, L:G.443, L:D.529 ADP.38: 24 residues within 4Å: Chain M: T.36, L.37, G.38, P.39, N.58, 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, L.472, I.487, E.489, K.494 Ligands: MG.37, BEF.39 18 PLIP interactions: 18 interactions with chain M Hydrogen bonds: M:G.38, M:G.91, M:G.91, M:T.92, M:T.92, M:T.93, M:S.94, M:S.94, M:S.94, M:S.162, M:S.162, M:S.163, M:G.404, M:G.405, M:E.489, M:K.494 Salt bridges: M:K.164, M:K.164 ADP.41: 20 residues within 4Å: Chain N: S.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, S.95, T.156, S.160, G.414, L.454, I.482, V.484, I.497, Q.499 Ligands: MG.40, BEF.42 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.40, N:G.92, N:T.93, N:T.94, N:T.94, N:S.95, N:S.95, N:S.95, N:S.160, N:G.414, N:G.415, N:V.484, N:Q.499, N:Q.499 Salt bridges: N:K.161 ADP.44: 24 residues within 4Å: Chain O: S.43, L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.162, S.165, S.166, K.167, G.421, G.422, G.423, L.462, L.502, E.512, V.517, E.519, K.524 Ligands: MG.43, BEF.45 18 PLIP interactions: 18 interactions with chain O Hydrogen bonds: O:G.45, O:G.97, O:G.97, O:G.97, O:T.99, O:T.99, O:S.100, O:S.165, O:S.165, O:S.166, O:G.422, O:G.423, O:E.512, O:E.519, O:K.524, O:K.524 Salt bridges: O:K.167, O:K.167 ADP.47: 22 residues within 4Å: Chain P: C.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.161, G.471, G.472, G.473, I.540, D.541, G.542, Y.553, I.555, E.557 Ligands: MG.46, BEF.48 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:G.40, P:G.92, P:G.92, P:T.93, P:T.94, P:T.94, P:T.95, P:T.95, P:T.161, P:G.472, P:G.473, P:G.542, P:Y.553, P:Y.553, P:E.557

16 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain A: D.58, G.59, D.89, G.90, T.91, T.92, K.161, D.397 Ligands: MG.1, ADP.2 No protein-ligand interaction detected (PLIP) BEF.6: 11 residues within 4Å: Chain B: D.67, A.68, G.97, D.98, G.99, T.100, N.101, K.170, D.403 Ligands: MG.4, ADP.5 No protein-ligand interaction detected (PLIP) BEF.9: 11 residues within 4Å: Chain C: N.64, D.65, G.66, G.95, D.96, T.98, T.99, K.169, D.395 Ligands: MG.7, ADP.8 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain D: N.85, D.86, D.117, G.118, T.119, T.120, K.191, D.425 Ligands: MG.10, ADP.11 No protein-ligand interaction detected (PLIP) BEF.15: 11 residues within 4Å: Chain E: T.36, N.58, D.59, G.60, D.90, T.92, T.93, K.164, D.386 Ligands: MG.13, ADP.14 No protein-ligand interaction detected (PLIP) BEF.18: 11 residues within 4Å: Chain F: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.396 Ligands: MG.16, ADP.17 No protein-ligand interaction detected (PLIP) BEF.21: 11 residues within 4Å: Chain G: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: MG.19, ADP.20 No protein-ligand interaction detected (PLIP) BEF.24: 10 residues within 4Å: Chain H: N.59, D.60, G.61, D.91, T.93, T.94, K.162, D.454 Ligands: MG.22, ADP.23 No protein-ligand interaction detected (PLIP) BEF.27: 11 residues within 4Å: Chain I: K.57, D.58, G.59, D.89, G.90, T.91, T.92, K.161, D.397 Ligands: MG.25, ADP.26 No protein-ligand interaction detected (PLIP) BEF.30: 11 residues within 4Å: Chain J: D.67, A.68, G.97, D.98, G.99, T.100, N.101, K.170, D.403 Ligands: MG.28, ADP.29 No protein-ligand interaction detected (PLIP) BEF.33: 11 residues within 4Å: Chain K: N.64, D.65, G.66, G.95, D.96, T.98, T.99, K.169, D.395 Ligands: MG.31, ADP.32 No protein-ligand interaction detected (PLIP) BEF.36: 10 residues within 4Å: Chain L: N.85, D.86, D.117, G.118, T.119, T.120, K.191, D.425 Ligands: MG.34, ADP.35 No protein-ligand interaction detected (PLIP) BEF.39: 11 residues within 4Å: Chain M: T.36, N.58, D.59, G.60, D.90, G.91, T.92, T.93, K.164 Ligands: MG.37, ADP.38 No protein-ligand interaction detected (PLIP) BEF.42: 11 residues within 4Å: Chain N: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.396 Ligands: MG.40, ADP.41 No protein-ligand interaction detected (PLIP) BEF.45: 11 residues within 4Å: Chain O: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: MG.43, ADP.44 No protein-ligand interaction detected (PLIP) BEF.48: 11 residues within 4Å: Chain P: C.38, N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.162 Ligands: MG.46, ADP.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leitner, A. et al., The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT. Structure (2012)

Release Date

2014-07-09

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 epsilon: DL
T-complex protein 1 subunit beta: EM
T-complex protein 1 subunit delta: FN
T-complex protein 1 subunit alpha: GO
T-complex protein 1 subunit gamma: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

I
N

B
H

J
P

C
G

K
O

D
E

L
M

E
B

M
J

F
D

N
L

G
A

O
I

H
C

P
K

T-complex protein 1 subunit zeta

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

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