8DD0: Native cardiac thin filament junction region
The structure of the native cardiac thin filament junction region. Determined by electron microscopy at 3.5 Å resolution. Released 28 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Sus scrofa
- Chains
- 16
- Atoms
- 22,892
- Mol. weight
- 587.52 kDa
- Ligands
- MG, ADP
- Released
- 28 Dec 2022
Explore 8DD0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DD0 contains 146 α-helices and 126 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A, B, C, D, E and F: 22 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| β-strand | 8 | 1 | 1 |
| β-strand | 11 | 1 | 2 |
| β-strand | 17-19 | 3 | 2 |
| β-strand | 21 | 1 | 1 |
| β-strand | 29-31 | 3 | 2 |
| β-strand | 35-38 | 4 | 3 |
| β-strand | 53-54 | 2 | 3 |
| α-helix | 55-59 | 5 | |
| α-helix | 62-64 | 3 | |
| β-strand | 65-68 | 4 | 3 |
| β-strand | 71 | 1 | 4 |
| β-strand | 76 | 1 | 4 |
| α-helix | 79-88 | 10 | |
| α-helix | 89-94 | 6 | |
| α-helix | 98-100 | 3 | |
| β-strand | 103-107 | 5 | 1 |
| α-helix | 113-125 | 13 | |
| β-strand | 131-136 | 6 | 1 |
| α-helix | 137-144 | 8 | |
| β-strand | 150-155 | 6 | 5 |
| β-strand | 160-166 | 7 | 5 |
| β-strand | 169-170 | 2 | 5 |
| α-helix | 172-174 | 3 | |
| β-strand | 176-178 | 3 | 5 |
| α-helix | 182-192 | 11 | |
| α-helix | 193-195 | 3 | |
| α-helix | 205-216 | 12 | |
| α-helix | 223-230 | 8 | |
| β-strand | 238-242 | 5 | 6 |
| β-strand | 245-250 | 6 | 6 |
| α-helix | 258-261 | 4 | |
| α-helix | 274-283 | 10 | |
| α-helix | 290-295 | 6 | |
| β-strand | 297-300 | 4 | 5 |
| α-helix | 302-305 | 4 | |
| α-helix | 309-320 | 12 | |
| β-strand | 329-330 | 2 | 5 |
| α-helix | 338-347 | 10 | |
| α-helix | 351-354 | 4 | |
| β-strand | 357-358 | 2 | 1 |
| α-helix | 359-365 | 7 | |
| α-helix | 367-369 | 3 | |
Chains G and L: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 233-281 | 49 | |
Chains H and M: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 231-281 | 51 | |
Chains I, J, N and O: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-69 | 67 | |
Chain K: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 98-104 | 7 | |
| α-helix | 106-156 | 51 | |
Chain P: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-89 | 5 | |
| α-helix | 98-104 | 7 | |
| α-helix | 106-124 | 19 | |
| α-helix | 127-155 | 29 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Actin, alpha cardiac muscle 1 | A, B, C, D, E, F | protein | 377 | Sus scrofa | P68137 (AlphaFold model) |
| Tropomyosin alpha-1 chain | G, H, I, J, L, M, N, O | protein | 284 | Sus scrofa | P42639 (AlphaFold model) |
| Troponin T2, cardiac type | K, P | protein | 295 | Sus scrofa | I3LS66 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8DD0_1 Actin, alpha cardiac muscle 1 (chains A, B, C, D, E, F)
MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
LSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIS
KQEYDEAGPSIVHRKCF
Sequence of entity 2 (G, H, I, J, L, M, N, O), FASTA
>8DD0_2 Tropomyosin alpha-1 chain (chains G, H, I, J, L, M, N, O)
MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKRLEDELVSLQKKLKATEDELDKY
SEAPKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAA
DESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAE
ERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAE
FAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHALNDMTSI
Sequence of entity 3 (K, P), FASTA
>8DD0_3 Troponin T2, cardiac type (chains K, P)
MSDVEETVDEYEEEQEEGAAEEEEAWRQDGDEQEEAVEEEAGGEAEAEEANAEEAGQEED
GREAEDGPMEESKPKPRLFMPNLVPPKIPDGERVDFDDIHRKRMKDLNELQTLIEAHFEN
RKKEEELVSLKDRIEKRRAERAEQQRIRTEREKERQTRLAEERARREEEENRRKAEDEAR
KKKALSNMMHFGGYIQKQAQTERKSGKRQTEREKKKKILAERRKVLAIDHLNEDQLREKA
KELWQSIYNLEAEKFDLQEKFKQQKYEINVLRNRINDNQKVSKTRGKAKVTGRWK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 6 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 6 |
Primary citation
High-resolution cryo-EM structure of the junction region of the native cardiac thin filament in relaxed state. Risi, C.M., Belknap, B., White, H.D. et al. PNAS Nexus (2023) 2:pgac298-pgac298. DOI 10.1093/pnasnexus/pgac298 · PubMed
Other PDB entries of the same protein (UniProt P68137 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4CBW 2.5 Å, Crystal structure of Plasmodium berghei actin I with D-loop from muscle actin
- 8EFH 3.3 Å, Helical reconstruction of the human cardiac actin-tropomyosin-myosin complex in complex…
- 7KO5 7.8 Å, Structure of cardiac native thin filament at pCa=5.8 having upper and lower troponins in…
- 7KOR 7.8 Å, Structure of cardiac native thin filament at pCa=5.8 having upper troponin in Ca2+ bound…
- 5NOL 8.0 Å, Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Closed" state
- 7KO4 8.0 Å, Structure of cardiac native thin filament at pCa=5.8 having upper and lower troponins in…
- 7TIJ 8.0 Å, Cardiac F-actin decorated with regulatory M-domain of cardiac myosin binding protein C
- 7TIT 8.0 Å, Cardiac thin filament decorated with regulatory M-domain of cardiac myosin binding…
- 7TJ7 8.0 Å, Cardiac thin filament decorated with C1 Ig-domain and regulatory M-domain of cardiac…
- 7KON 8.1 Å, Structure of upper Tn Ca2+ free (rotated) and lower Tn Ca2+ bound cardiac native thin…
- 7KO7 8.3 Å, Structure of the native cardiac thin filament at pCa=5.8 having upper Tn in Ca2+ free…
- 5NOG 11.0 Å, Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Blocked" state
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