Near-atomic resolution for one state of F-actin

Abstract

Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural heterogeneity. We have used a direct electron detector, cryo-electron microscopy, and the forces imposed on actin filaments in thin films to reconstruct one state of the filament at 4.7 Å resolution, which allows for building a reliable pseudo-atomic model of F-actin. We also report a different state of the filament where actin protomers adopt a conformation observed in the crystal structure of the G-actin-profilin complex with an open ATP-binding cleft. Comparison of the two structural states provides insights into ATP-hydrolysis and filament dynamics. The atomic model provides a framework for understanding why every buried residue in actin has been under intense selective pressure.

Fig. 1

3D-reconstruction of frozen hydrated actin filaments. (A) Typical micrograph of actin filaments embedded in thin ice. (B) Stereo view of the 3D-reconstruction at ~ 4.7 Å resolution. (C) The absence of the N-terminal density in the map is indicated with a black arrow, while the hydrophobic plug density is marked with a green arrow.

Fig. 2

Visual inspection of the map supports the resolution estimated. (A) A close-up view of the β-sheet in SD3 shows that the strands are resolved. ILE330 (red), Pro172 (green), Tyr166 (yellow) and Lys328 (magenta) are highlighted. (B) The region surrounding the ADP (red) is shown.

Fig. 3

Interface between actin protomers in the canonical structural state of F-actin. (A) Interface between SD3 and SD4 is composed of three pairs of interacting residues: 245–322, 324–241, and 244–325. Residues in SD4 of the lower protomer are in red, while residues in SD3 of the upper protomer are in blue. Black arrow indicates a bridge of density between residues 241 and 324. Pro243 that forms a kink in the top of the loop and is believed to position Asp241 and Asp244 is shown in orange. (B) Side-chains of residues 205 (in red) and 286 (in blue) are seen in the map and are not involved in the SD3/SD4 interactions. (C) Interface between SD2 of the lower protomer (red residues) and SD1/3 of the upper protomer (blue residues) includes contacts between residues 44 and 143, 47 and 352, 61 and 167, 62 and 288, and finally 64 and166. Red arrow indicates a contact between residues 44 and 143, while the red arrowhead marks a contact between residues 47 and 352. (D) Pro38 (red) makes a bridge of density with Tyr169 in blue (blue arrow), while Tyr53 (cyan) makes an interaction with Lys84 which is in magenta (magenta arrow). (E) Hydrophobic plug does not make any strong specific interactions with protomers in the opposite strand. There are hydrogen bonds between Val201/Thr202 (in red) and Ser271 (in magenta), along with a hydrophobic interaction between His173 (in cyan) and Ile267 (in blue) (F) Lateral contacts between the two strands contain two pairs of interacting residues: 113–195, and 111–194. Residues in SD1 are in blue, while residues in SD4 are in red.

Fig. 4

Comparison of canonical F-actin (A) with T1-actin (B) and T2-actin (C). The four subdomains of actin (SD1-SD4) are labeled 1–4. The bottom panels in A–C are the same 3D-reconstructions rotated by 90 degrees. Actin protomers are shown in different colors. All 3D-reconstructions are filtered to 12 Å resolution. (D) Transition from canonical actin (red) to T1-actin (cyan) involves a rotation of SD4/SD3 by ~15° around the hinge region (black arrow). (E) Transition from T1-actin (cyan) to T2-actin (blue) mainly involves transition of the 197–215 region of SD4 (magenta) towards SD2 (red arrow). (F) Alignment of T2-protomer (blue) with the crystal structure of actin in the open state (Chik et al., 1996).

Fig. 5

Interface between actin protomers in T1- and T2- actins. 3D-reconstructions are front (A and C) and side (B, D and E) views. (A) Longitudinal contacts in T1-actin reside in the 39–47 region located in SD2 of the lower protomer (red) and region 285–291 (blue) in SD3 of the upper protomer. (B) Lateral interactions are likely to involve residues 112–118 (orange) and 368–371 (green) in SD1 of the upper protomer, and 195–205 (magenta) in SD4 along with the hydrophobic plug (264–272 in cyan) in the lower protomer. (C) Longitudinal contacts in T2-actin are similar to the T1-actin, but also may include residue 60–64 (marked in red). (D) lateral interactions in T2-actin map to the same regions as in T1-actin except for the112–118 region. (E) Residues linked to human diseases are shown as spheres in different colors. Note that these residues are at the interfaces between protomers in the tilted actin.

Fig. 6

A comparison between the antiparallel actin dimer 1LCU (Bubb et al., 2002) and two states of the actin filament. A) When chain A of the dimer (in yellow) is superimposed upon one subunit (red) in our model for canonical F-actin (1.1 A rmsd, over 236 Cα pairs), the second chain of the dimer (in green) makes extensive clashes with another protomer in the filament (arrow). B) When the same chain A of 1LCU (in yellow) is superimposed upon a protomer in the T1 actin (in red) (1.3 A rmsd, over 242 Cα pairs), the second chain of the dimer (in green) makes no significant clashes with the filament.

Fig. 7

Comparison of the nucleotide position in the ATP-binding cleft of the canonical, T1 and T2 actins. (A) Back view of the actin molecule with domains numbered in black. Black square marks the ATP-binding cleft magnified in B–D. (B) Atomic model of the actin-ADP interaction derived from the 4.7 Å 3D-reconstruction of the canonical F-actin. (C) Modeling of the nucleotide interaction with the T1 protomer. (D) Modeling of the nucleotide interaction with the T2 protomer. (B–C) The base of the nucleotide interacts with Lys213 and Gln302 marked in blue. Phosphate groups are coordinated through the interaction with Ser14, Glu15, and Leu16 of the SD1 (in cyan), and Asp157 (magenta) and Val159 (green) located in SD3. Divalent metal ion interacts with phosphate groups on the top, and Gln137 and Asp154 on the bottom (in purple). The distances between the nucleotide base and Lys213 are shown as orange arrows, distances between the Mg²⁺ ion and Gln137 are shown as magenta arrows, while the distances between Ser14 and Val159 that coordinate terminal phosphate are marked with black arrows.