SMTL ID : 3g37.1

Cryo-EM structure of actin filament in the presence of phosphate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.14, S.15, G.16, L.17, K.19, G.157, D.158, A.182, G.183, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.15, A:G.16, A:L.17, A:G.157, A:D.158, A:R.211, A:K.214, A:G.303, A:T.304 Salt bridges: A:K.19, A:K.19 ADP.12: 18 residues within 4Å: Chain B: G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.15 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.15, B:G.16, B:L.17, B:D.158, B:D.158, B:R.211, B:K.214, B:E.215, B:E.215, B:G.303, B:T.304 Salt bridges: B:K.19, B:K.19 ADP.20: 18 residues within 4Å: Chain C: G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.23 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.15, C:G.16, C:L.17, C:D.158, C:D.158, C:R.211, C:K.214, C:G.303, C:T.304 Salt bridges: C:K.19, C:K.19 ADP.32: 16 residues within 4Å: Chain D: G.14, S.15, G.16, L.17, K.19, G.157, D.158, R.211, K.214, E.215, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.35 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.15, D:G.16, D:L.17, D:D.158, D:D.158, D:R.211, D:K.214, D:G.303, D:T.304 Salt bridges: D:K.19, D:K.19 ADP.41: 15 residues within 4Å: Chain E: G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.44 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.16, E:L.17, E:D.158, E:D.158, E:R.211, E:K.214, E:G.303, E:T.304 Salt bridges: E:K.19, E:K.19 ADP.54: 18 residues within 4Å: Chain F: D.12, G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.57 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.15, F:G.16, F:L.17, F:D.158, F:D.158, F:R.211, F:K.214, F:G.303, F:T.304 Salt bridges: F:K.19, F:K.19 ADP.62: 20 residues within 4Å: Chain G: G.14, S.15, G.16, L.17, K.19, S.156, G.157, D.158, A.182, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.65 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:S.15, G:G.16, G:L.17, G:D.158, G:D.158, G:R.211, G:K.214, G:G.303, G:T.304 Salt bridges: G:K.19, G:K.19 ADP.72: 19 residues within 4Å: Chain H: G.14, S.15, G.16, L.17, K.19, G.157, D.158, A.182, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.75 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:S.15, H:G.16, H:L.17, H:G.157, H:D.158, H:R.211, H:K.214, H:E.215, H:G.303 Salt bridges: H:K.19, H:K.19 ADP.82: 18 residues within 4Å: Chain I: G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.85 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:S.15, I:G.16, I:L.17, I:G.157, I:D.158, I:R.211, I:K.214, I:G.303, I:T.304 Salt bridges: I:K.19, I:K.19 ADP.93: 17 residues within 4Å: Chain J: G.14, S.15, G.16, L.17, K.19, G.157, D.158, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.96 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:S.15, J:G.16, J:L.17, J:D.158, J:D.158, J:R.211, J:K.214, J:G.303 Salt bridges: J:K.19, J:K.19 pi-Stacking: J:Y.307 ADP.102: 18 residues within 4Å: Chain K: G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.105 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:S.15, K:G.16, K:L.17, K:G.157, K:D.158, K:R.211, K:K.214, K:E.215, K:E.215, K:G.303, K:T.304 Salt bridges: K:K.19, K:K.19 ADP.113: 18 residues within 4Å: Chain L: G.14, S.15, G.16, L.17, K.19, G.157, D.158, G.183, R.211, K.214, E.215, G.302, G.303, T.304, M.306, Y.307, K.337 Ligands: MG.116 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:S.15, L:G.16, L:L.17, L:D.158, L:D.158, L:R.211, L:K.214, L:E.215, L:G.303, L:T.304 Salt bridges: L:K.19, L:K.19

36 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: D.188, M.191, R.207 Ligand excluded by PLIP PO4.3: 3 residues within 4Å: Chain A: Y.219, K.239, R.255 Ligand excluded by PLIP PO4.10: 4 residues within 4Å: Chain A: T.203 Chain B: D.185 Chain C: K.285 Ligands: MG.7 Ligand excluded by PLIP PO4.11: 2 residues within 4Å: Chain A: D.185 Chain B: K.285 Ligand excluded by PLIP PO4.13: 3 residues within 4Å: Chain B: D.188, M.191, R.207 Ligand excluded by PLIP PO4.14: 2 residues within 4Å: Chain B: K.239, R.255 Ligand excluded by PLIP PO4.21: 2 residues within 4Å: Chain C: D.188, M.191 Ligand excluded by PLIP PO4.22: 3 residues within 4Å: Chain C: L.237, K.239, R.255 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain C: T.203 Chain D: D.185 Chain E: K.285 Ligands: MG.27 Ligand excluded by PLIP PO4.31: 5 residues within 4Å: Chain B: V.202, T.203 Chain C: D.185 Chain D: K.285 Ligands: MG.26 Ligand excluded by PLIP PO4.33: 3 residues within 4Å: Chain D: D.188, M.191, R.207 Ligand excluded by PLIP PO4.34: 3 residues within 4Å: Chain D: Y.219, K.239, R.255 Ligand excluded by PLIP PO4.42: 3 residues within 4Å: Chain E: D.188, M.191, R.207 Ligand excluded by PLIP PO4.43: 3 residues within 4Å: Chain E: Y.219, K.239, R.255 Ligand excluded by PLIP PO4.50: 4 residues within 4Å: Chain E: T.203 Chain F: D.185 Chain G: K.285 Ligands: MG.47 Ligand excluded by PLIP PO4.52: 5 residues within 4Å: Chain D: V.202, T.203 Chain E: D.185 Chain F: K.285 Ligands: MG.38 Ligand excluded by PLIP PO4.53: 4 residues within 4Å: Chain F: T.203 Chain G: D.185 Chain H: K.285 Ligands: MG.60 Ligand excluded by PLIP PO4.55: 3 residues within 4Å: Chain F: D.188, M.191, R.207 Ligand excluded by PLIP PO4.56: 3 residues within 4Å: Chain F: L.237, K.239, R.255 Ligand excluded by PLIP PO4.63: 3 residues within 4Å: Chain G: D.188, M.191, R.207 Ligand excluded by PLIP PO4.64: 3 residues within 4Å: Chain G: Y.219, K.239, R.255 Ligand excluded by PLIP PO4.71: 4 residues within 4Å: Chain G: T.203 Chain H: D.185 Chain I: K.285 Ligands: MG.68 Ligand excluded by PLIP PO4.73: 3 residues within 4Å: Chain H: D.188, M.191, R.207 Ligand excluded by PLIP PO4.74: 3 residues within 4Å: Chain H: Y.219, K.239, R.255 Ligand excluded by PLIP PO4.83: 3 residues within 4Å: Chain I: D.188, M.191, R.207 Ligand excluded by PLIP PO4.84: 2 residues within 4Å: Chain I: K.239, R.255 Ligand excluded by PLIP PO4.90: 4 residues within 4Å: Chain I: V.202, T.203 Chain K: K.285 Ligands: MG.87 Ligand excluded by PLIP PO4.92: 3 residues within 4Å: Chain H: T.203 Chain J: K.285 Ligands: MG.78 Ligand excluded by PLIP PO4.94: 3 residues within 4Å: Chain J: D.188, M.191, R.207 Ligand excluded by PLIP PO4.95: 4 residues within 4Å: Chain J: Y.219, L.237, K.239, R.255 Ligand excluded by PLIP PO4.103: 3 residues within 4Å: Chain K: D.188, M.191, R.207 Ligand excluded by PLIP PO4.104: 4 residues within 4Å: Chain K: Y.219, L.237, K.239, R.255 Ligand excluded by PLIP PO4.110: 4 residues within 4Å: Chain K: V.202, T.203 Chain L: D.185 Ligands: MG.107 Ligand excluded by PLIP PO4.112: 4 residues within 4Å: Chain J: T.203 Chain K: D.185 Chain L: K.285 Ligands: MG.98 Ligand excluded by PLIP PO4.114: 3 residues within 4Å: Chain L: D.188, M.191, R.207 Ligand excluded by PLIP PO4.115: 3 residues within 4Å: Chain L: Y.219, K.239, R.255 Ligand excluded by PLIP

72 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain A: D.12, Q.138 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: D.287, I.288, D.289 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.287, A:D.289 MG.6: 4 residues within 4Å: Chain A: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.266 MG.7: 1 residues within 4Å: Ligands: PO4.10 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: Q.355 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Q.355 MG.9: 1 residues within 4Å: Chain A: D.223 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain B: D.12 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain B: D.287, I.288, D.289 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.287, B:D.289 MG.17: 4 residues within 4Å: Chain B: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.266 MG.18: 1 residues within 4Å: Chain B: Q.355 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.355 MG.19: 1 residues within 4Å: Chain B: D.223 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain C: D.12 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.24: 7 residues within 4Å: Chain A: Q.60, S.61, R.63, E.208 Chain C: D.287, I.288, D.289 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.287, C:D.287, C:D.289, A:E.208 MG.25: 3 residues within 4Å: Chain C: Q.264, S.266, S.272 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.266 MG.26: 1 residues within 4Å: Ligands: PO4.31 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain C: E.206 Ligands: PO4.30 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain C: Q.355 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Q.355 MG.29: 1 residues within 4Å: Chain C: D.223 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain D: D.12, Q.138 Ligands: ADP.32 No protein-ligand interaction detected (PLIP) MG.36: 5 residues within 4Å: Chain B: R.63, E.208 Chain D: D.287, I.288, D.289 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:E.208, D:D.289 MG.37: 4 residues within 4Å: Chain D: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.266 MG.38: 1 residues within 4Å: Ligands: PO4.52 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain D: Q.355, W.357 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:Q.355 MG.40: 1 residues within 4Å: Chain D: D.223 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Ligands: ADP.41 No protein-ligand interaction detected (PLIP) MG.45: 4 residues within 4Å: Chain C: R.63, E.208 Chain E: I.288, D.289 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Metal complexes: E:D.289, E:D.289, C:E.208 MG.46: 4 residues within 4Å: Chain E: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.266 MG.47: 1 residues within 4Å: Ligands: PO4.50 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain E: Q.355, W.357 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:Q.355 MG.49: 1 residues within 4Å: Chain E: D.223 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain F: D.223, E.317 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain F: D.12 Ligands: ADP.54 No protein-ligand interaction detected (PLIP) MG.58: 6 residues within 4Å: Chain D: Q.60, S.61, R.63 Chain F: D.287, I.288, D.289 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.287, F:D.289 MG.59: 4 residues within 4Å: Chain F: Q.264, S.266, M.270, S.272 No protein-ligand interaction detected (PLIP) MG.60: 1 residues within 4Å: Ligands: PO4.53 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain F: Q.355 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:Q.355 MG.65: 2 residues within 4Å: Chain G: D.12 Ligands: ADP.62 No protein-ligand interaction detected (PLIP) MG.66: 6 residues within 4Å: Chain E: S.61, R.63, E.208 Chain G: D.287, I.288, D.289 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Metal complexes: G:D.287, G:D.289, E:E.208 MG.67: 4 residues within 4Å: Chain G: Q.264, S.266, M.270, S.272 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain H: R.184 Ligands: PO4.71 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain G: Q.355, W.357 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:Q.355 MG.70: 1 residues within 4Å: Chain G: D.223 No protein-ligand interaction detected (PLIP) MG.75: 2 residues within 4Å: Chain H: D.12 Ligands: ADP.72 No protein-ligand interaction detected (PLIP) MG.76: 5 residues within 4Å: Chain F: R.63, E.208 Chain H: D.287, I.288, D.289 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F Metal complexes: H:D.287, H:D.289, F:E.208 MG.77: 4 residues within 4Å: Chain H: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.266 MG.78: 1 residues within 4Å: Ligands: PO4.92 No protein-ligand interaction detected (PLIP) MG.79: 2 residues within 4Å: Chain H: Q.355, W.357 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:Q.355 MG.80: 1 residues within 4Å: Chain H: D.223 No protein-ligand interaction detected (PLIP) MG.81: 4 residues within 4Å: Chain I: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.266 MG.85: 1 residues within 4Å: Ligands: ADP.82 No protein-ligand interaction detected (PLIP) MG.86: 7 residues within 4Å: Chain G: Q.60, S.61, R.63, E.208 Chain I: D.287, I.288, D.289 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain I Metal complexes: G:E.208, I:D.287, I:D.289 MG.87: 1 residues within 4Å: Ligands: PO4.90 No protein-ligand interaction detected (PLIP) MG.88: 1 residues within 4Å: Chain I: Q.355 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:Q.355 MG.89: 2 residues within 4Å: Chain I: D.223, E.317 No protein-ligand interaction detected (PLIP) MG.91: 4 residues within 4Å: Chain J: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.266 MG.96: 2 residues within 4Å: Chain J: D.12 Ligands: ADP.93 No protein-ligand interaction detected (PLIP) MG.97: 6 residues within 4Å: Chain H: Q.60, R.63, E.208 Chain J: D.287, I.288, D.289 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain J Metal complexes: H:E.208, J:D.289, J:D.289 MG.98: 3 residues within 4Å: Chain J: E.206 Chain K: R.184 Ligands: PO4.112 No protein-ligand interaction detected (PLIP) MG.99: 1 residues within 4Å: Chain J: Q.355 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:Q.355 MG.100: 2 residues within 4Å: Chain J: D.223, R.313 No protein-ligand interaction detected (PLIP) MG.101: 4 residues within 4Å: Chain K: Q.264, S.266, M.270, S.272 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.266 MG.105: 2 residues within 4Å: Chain K: D.12 Ligands: ADP.102 No protein-ligand interaction detected (PLIP) MG.106: 7 residues within 4Å: Chain I: Q.60, S.61, R.63, E.208 Chain K: D.287, I.288, D.289 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I Metal complexes: K:D.287, K:D.289, I:E.208 MG.107: 2 residues within 4Å: Chain K: E.206 Ligands: PO4.110 No protein-ligand interaction detected (PLIP) MG.108: 1 residues within 4Å: Chain K: Q.355 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:Q.355 MG.109: 2 residues within 4Å: Chain K: D.223, E.317 No protein-ligand interaction detected (PLIP) MG.111: 3 residues within 4Å: Chain L: Q.264, S.266, S.272 No protein-ligand interaction detected (PLIP) MG.116: 2 residues within 4Å: Chain L: D.12 Ligands: ADP.113 No protein-ligand interaction detected (PLIP) MG.117: 7 residues within 4Å: Chain J: Q.60, S.61, R.63, E.208 Chain L: D.287, I.288, D.289 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J Metal complexes: L:D.287, L:D.289, L:D.289, J:E.208 MG.118: 1 residues within 4Å: Chain L: E.206 No protein-ligand interaction detected (PLIP) MG.119: 1 residues within 4Å: Chain L: Q.355 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:Q.355 MG.120: 2 residues within 4Å: Chain L: D.223, R.313 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, K. et al., Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell(Cambridge,Mass.) (2010)

Release Date

2010-11-03

Peptides

Actin, alpha skeletal muscle: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

E
S

F
T

G
U

H
V

I
W

J
X

K
Y

L
Z

Actin, alpha skeletal muscle