SMTL ID : 9mox.1

Structure of native murine cardiac thin filament variant I79N in troponin T at pCa=5.8 in Ca2+-bound partially activated state (lower strand)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-2-4-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.16, A:D.159, A:D.159, A:K.215, A:G.304 Salt bridges: A:K.20, A:K.20 ADP.3: 16 residues within 4Å: Chain B: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:D.159, B:D.159, B:K.215, B:G.304 Salt bridges: B:K.20, B:K.20 ADP.5: 16 residues within 4Å: Chain C: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.16, C:D.159, C:D.159, C:K.215, C:G.304 Salt bridges: C:K.20, C:K.20 ADP.7: 16 residues within 4Å: Chain D: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.16, D:D.159, D:D.159, D:K.215, D:G.304 Salt bridges: D:K.20, D:K.20 ADP.9: 16 residues within 4Å: Chain E: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.16, E:D.159, E:D.159, E:K.215, E:G.304 Salt bridges: E:K.20, E:K.20 ADP.11: 16 residues within 4Å: Chain F: G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.12 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.16, F:D.159, F:D.159, F:K.215, F:G.304 Salt bridges: F:K.20, F:K.20

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.139, D.156 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.139, D.156 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.139, D.156 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.139, D.156 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.139, D.156 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: Q.139, D.156 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.13: 7 residues within 4Å: Chain G: I.61, D.65, D.67, G.68, S.69, G.70, T.71 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.67, G:T.71 CA.14: 9 residues within 4Å: Chain G: G.140, D.141, K.142, N.143, N.144, D.145, G.146, R.147, E.152 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:G.140, G:D.141, G:D.145 CA.15: 7 residues within 4Å: Chain G: D.105, N.107, D.109, Y.111, I.112, D.113, E.116 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.105, G:Y.111, G:E.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Risi, C.M. et al., The role of the troponin T interactions with actin in regulation of cardiac thin filament revealed by the troponin T pathogenic variant Ile79Asn. J.Mol.Cell.Cardiol. (2025)

Release Date

2025-06-04

Peptides

Actin, alpha cardiac muscle 1: ABCDEF
Troponin C, slow skeletal and cardiac muscles: G
Troponin I, cardiac muscle: H
Isoform 6 of Troponin T, cardiac muscle: IJ
Tropomyosin alpha-1 chain: KLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Actin, alpha cardiac muscle 1

Troponin C, slow skeletal and cardiac muscles

Troponin I, cardiac muscle

Isoform 6 of Troponin T, cardiac muscle

Tropomyosin alpha-1 chain

Related Entries With Identical Sequence